Nélida Abarca

Introduction : DNA metabarcoding is currently under intense scrutiny for its future implementation in biodiversity monitoring and ecological assessment, particularly within the EU Water Framework Directive (WFD). However, before metabarcoding can be deployed for WFD reporting, challenges such as the incompleteness of reference databases need to be addressed. In this context, this study presents the results of a national barcoding project (FRESHBAR) focusing on benthic freshwater diatoms of Sweden, a key organism group regarding both ecology and environmental assessment. One major goal of the project was the publication and vouchering of all data, material, and results. Methods : A total of 312 diatom cultures were established, with a focus on oligotrophic and acid habitats. The cultures were sequenced for two barcodes ( rbc L and 18SV4) and identified using light microscopy; selected strains were also studied by scanning electron microscopy. All data, including sampling metadata, barcode sequences, images, and voucher material, were published following the FAIR principles. Some cultures were archived in diatom culture collections. Results : Almost all strains were successfully sequenced and identified as 51 taxa across 17 genera, with the highest diversity in the genera Eunotia and Fragilaria . An attempt was also made to identify all taxa at the species level. Approximately half of the taxa were new to Diat.barcode, a curated diatom reference database. Conclusion : FRESHBAR represents the first large-scale effort to generate barcode reference sequences for Nordic benthic freshwater diatoms. As all data are publicly available, the added sequences and morphological information will help identify all taxa properly to the species level, unravel taxon relationships within diatoms, and improve reference databases for environmental monitoring and research.

Diatoms are of major importance in marine and freshwater systems, but their occurrence in terrestrial situations is generally thought to be exceptional. Following up on the accidental discovery of epiphytic diatoms on bark samples in an unrelated study, we investigated their presence in the tropical lowlands of Panama more systematically using scanning electron and light microscopy. We sampled inundated and aerial bark portions of Annona glabra, a tree that grows along the shore of Lake Gatun, and took bark samples from other tree and liana species at c. 1.5 m height in the forest understory. In total, we found 70 diatom taxa in 28 genera. Species numbers and composition differed among the three microhabitats with the largest numbers on inundated bark portions, but even in the forest understory, we found 12 taxa with densities of up to 900 frustules per mm⁻² of bark. Our data set is still quite limited in scale but the results suggest the possibility that hitherto unacknowledged assemblages of epiphytic diatoms may be quite common in wet tropical forests, which clearly warrants further study.

The Euphrates-Tigris catchment area is one of the major drainage basins in the Middle East but climate change, overuse of waters and subsequent salinization has brought this region to the brink of ecological devastation. The aim of this study was to investigate the biodiversity of epiphytic diatoms in Iraq, for the first time using a combination of morphological and metabarcoding methods. 47 samples were collected at six sampling sites along the Rivers Tigris and Euphrates in northern Basra, Southern Iraq, during the summer of 2019 (dry season) and winter of 2020 (rainy season). The composition of the epiphytic diatoms in each sample was compared with both methods. The microscopic-morphological analysis of the environmental samples resulted in the identification of 284 infrageneric taxa in 59 genera. For the metabarcoding analysis the V4 region of the 18S marker gene was used and resulted in 1454 ASVs (Amplicon sequence variants) comprising 54 genera and 108 species with several ASVs belonging to the same taxa. The non-metric multidimensional scaling (NMDS) plots for morphology showed a clear seasonal effect in the diatom community composition, while the NMDS plots for 18SV4 analyses did not show a seasonal effect in community composition for the same samples. The incomplete taxonomic reference database for the studied sites turned out to be the major limitation of the molecular approach. Nevertheless, the combination of morphological and molecular methods increased the detection and identification of the diatom assemblages and laid the foundation for understanding their biodiversity in this region.

In a floristic paper by Kryvosheia & Kasputin (2019), Iconella amphioxys (W.Sm.) D.Kasputin & Kryvosheia was proposed as a new combination for Surirella amphioxys W.Sm. Aim of our correspondence is a taxonomic evaluation of its identity, classification, as well as an assessment of knowledge gaps by comparing different resources (English 2011, Hofmann et al. 2011, Jahn et al. 2017, Krammer and Lange-Bertalot 1988, Lange-Bertalot et al. 2017, Lange-Bertalot and Krammer 1987, Ruck et al. 2016, Smith 1856).

Polar regions are among the most extreme habitats on Earth. However, diatom biodiversity in those regions is much more extensive and ecologically diverse than previously thought. The objective of this study was to add knowledge to benthic diatom biodiversity in Western Antarctic coastal zones via identification by means of morphology, DNA metabarcoding and cultured isolates. In addition, a taxonomically validated reference library for Antarctic benthic diatoms was established with comprehensive information on habitat, morphology and DNA barcodes (rbcL and 18SV4). Benthic samples from marine, brackish and freshwater habitats were taken at the Antarctic Peninsula. A total of 162 clonal cultures were established, resulting in the identification of 60 taxa. The combination of total morphological richness of 174 taxa, including the clones, with an additional 73 taxa just assigned by metabarcoding resulted in 247 infrageneric taxa. Of those taxa, 33 were retrieved by all three methods and 111 only by morphology. The barcode reference library of Antarctic species with the new references obtained through culturing allowed the assignment of 47 taxa in the metabarcoding analyses, which would have been left unassigned because no matching reference sequences were available before. Non–metric multidimensional scaling analyses of morphological as well as molecular data showed a clear separation of diatom communities according to water and substratum types. Many species, especially marine taxa, still have no record in reference databases. This highlights the need for a more comprehensive reference library to further improve routine diatom metabarcoding. Overall, a combination of morphological and molecular methods, along with culturing, provides complementary information on the biodiversity of benthic diatoms in the region.

Monoclonal diatom strains are the basis for integrative taxonomical studies combining molecular and morphological data for better taxonomic resolution and identification. The identification of diatoms, based on morphological features of the frustule, is difficult due to the variability of characters within and amongst species. The longer the cultivation time, the more cell size is reduced during asexual reproduction. Many divisions of the cell complicate identification as morphological characters of the frustule change at different rates in different taxa and teratologies can develop. Morphological variability raises the question whether the investigated genetic markers are stable over the cultivation time span. Sixteen monoclonal pennate diatom strains, identified as 10 different species in six genera, were cultivated for up to 18 or 24 months. It was shown that molecular data for the 18S-V4, rbcL, and psbA markers were stable for the entire cultivation time of all taxa. Images of the valves of the strains were taken every six months and examined morphometrically. Depending on the time since the start of the cultures, the morphological features showed high variability, particularly in length and shape, whereas width and number of striae, costae or fibulae were more stable, depending on the taxon and strain. A limited time span and good culture conditions seem to be prerequisite to avoid the production of teratological frustules. The results of parallel cultures in a unique experimental design are compared to observations from the literature dealing with single strains or special cognitive interests.

Temperature and salinity are some of the most influential abiotic parameters shaping biota in aquatic ecosystems. In recent decades, climate change has had a crucial impact on both factors—especially around the Antarctic Peninsula—with increasing air and water temperature leading to glacial melting and the accompanying freshwater increase in coastal areas. Antarctic soft and hard bottoms are typically inhabited by microphytobenthic communities, which are often dominated by benthic diatoms. Their physiology and primary production are assumed to be negatively affected by increased temperatures and lower salinity. In this study, six representative benthic diatom strains were isolated from different aquatic habitats at King George Island, Antarctic Peninsula, and comprehensively identified based on molecular markers and morphological traits. Photosynthesis, respiration, and growth response patterns were investigated as functions of varying light availability, temperature, and salinity. Photosynthesis–irradiance curve measurements pointed to low light requirements, as light-saturated photosynthesis was reached at −2 s⁻¹. The marine isolates exhibited the highest effective quantum yield between 25 and 45 S_A (absolute salinity), but also tolerance to lower and higher salinities at 1 S_A and 55 S_A, respectively, and in a few cases even A. In contrast, the limnic isolates showed the highest effective quantum yield at salinities ranging from 1 S_A to 20 S_A. Almost all isolates exhibited high effective quantum yields between 1.5 °C and 25 °C, pointing to a broad temperature tolerance, which was supported by measurements of the short-term temperature-dependent photosynthesis. All studied Antarctic benthic diatoms showed activity patterns over a broader environmental range than they usually experience in situ. Therefore, it is likely that their high ecophysiological plasticity represents an important trait to cope with climate change in the Antarctic Peninsula.

In central Mexico, streams flow from mountain protected areas at high elevations, i.e. abive 2,400 m a.s.l., being exposed to different human activities along their course. The main human threats of these aquatic ecosystems include the presence of hydraulic infrastructure (e.g. canals and dams), the construction of bridges or roads, fish farming, agriculture, livestock, unregulated tourism or irregular human settlements, resulting in nutrient enrichment, organic pollution and low hydromorphological quality. Diatoms, widely recognized as valuable indicators of environmental conditions, offer a unique opportunity to assess the ecological quality of the streams in and around this megacity, as they respond directly and sensitively to specific physical, chemical and biological changes. To conduct ecological assessment, the composition of diatom communities has traditionally been characterized by morphological methods and most recently by environmental DNA (eDNA) metabarcoding. However, the diatom communities of only a few of these streams in the Basin of Mexico have been characterized morphologically at low resolution light microscopy (LM), and no eDNA-based studies have been conducted yet. In this context, our aims are to 1) implement morphological and eDNA metabarcoding methods for the identification and quantification of epilithic diatoms and to assess their seasonal and spatial response in three peri-urban mountain streams from the Basin of Mexico, and 2) develop a metric to assess and monitor the ecological quality in these streams. For this purpose, we characterized a) the physical, environmental and hydro-morphological conditions related to ecosystem quality, and b) the diatom diversity and community structure of nine sites per stream (27 sites). The sites include headwaters, as well as middle and lower reaches with different land-use and anthropologic pressures, and were investigated over three hydrological periods, i.e. post-rainy, dry-cold and dry-warm. Species identification was first conducted under LM and scanning electron microscopy (SEM), and is currently been done by eDNA metabarcoding of the V4 region of the 18S rRNA gene and a fragment of the chloroplast marker rbcL. Our study has resulted in 520 infrageneric taxa identified by LM and SEM, the largest diversity ever found for freshwater diatoms of Mexico. From this data, we found a clear environmental gradient from almost pristine conditions towards heavily polluted states as the streams enter the city. These changes are well reflected by variations in the diatom community structure, as revealed by the Diatom Ecological Quality Index (DEQI), newly developed to evaluate the ecological quality of the streams in and around this megacity.

In order to understand the taxonomy and phylogeny of the genus Gomphonema, the type of the name of the genus, G. acuminatum, and related species complexes are studied with an integrative taxonomic approach. Sixty-seven unialgal Gomphonema strains were established from 34 different water bodies in Croatia, Faroe Islands, Finland, Iceland, Germany, Mexico, Spain, Switzerland and Korea, which provided molecular (18S and rbcL), morphometric and ultrastructural data. Our study was complemented by molecular data from INSDC, summing up the studied data to 82 freshwater Gomphonema strains from the G. acuminatum and related species complexes which are here defined as the Gomphonema core group. Except for outline variations which occur even within one clone, their micro-morphologies are indistinguishable. The molecular data of the two markers clustered the taxa of the core group into one clade, well differentiated from other Gomphonema taxa such as G. augur and G. parvulum. For differentiation within the clade, the plastid marker rbcL provided better species resolution comparable to traditionally recognized taxa. The combined analysis of the molecular as well as morphological data resulted in the defining of only 7 subclades in contrast to 20 currently assigned names for the taxa of the Gomphonema core group in this study. The Gomphonema core group has been overdescribed due to the use of outline as the main criterion for species delimitation. A polyphasic approach, combining molecular and micromorphological data for taxonomy, nomenclatural evaluation, and observations from clonal cultures can reveal the full intricacies of evolutionary relations.

Background and aims – Within the project “German Barcode of Life – Diatoms” common diatoms of German waters were routinely isolated and cultivated. In order to understand the taxonomy and phylogeny of the genus Gomphonema, one of the most common taxa of Central Europe, known currently either under the name Gomphonema olivaceum in Europe or Gomphoneis olivacea in America, was studied. Methods – Twenty unialgal strains were established from five different water bodies in Germany and one from Lake Balaton, Hungary, which supplied molecular data (18S V4 and rbcL) besides morphometric and ultrastructural data. In addition, on eight populations from different water bodies including the type from Denmark, morphometric and micromorphological studies by light and scanning electron microscopy were performed. Key results – Molecular and micromorphological data show that the target taxon neither belongs to Gomphonema Ehrenb. nor to Gomphoneis Cleve. By reinstating the genus name Gomphonella Rabenh., the nomenclatural and taxonomic enigma of this taxon is solved, and with the presentation of the type by Hornemann the authorship of the epithet is clarified. Molecular data for the unialgal strains and several environmental clones show that there is more diversity in the Gomphonella olivacea clade than can be identified morphologically. In addition, the establishment of the new species Gomphonella coxiae and Gomphonella acsiae is supported. The molecular data classified Gomphonella species as belonging to the Cymbellales but not to the Gomphonemataceae. In addition, molecular data put Gomphoneis tegelensis R.Jahn & N.Abarca also into Gomphonella. In order to make the genera Gomphoneis and Gomphonema monophyletic, their astigmate members are transferred to Gomphonella. Conclusions – The results clarify that the gomphonemoid outline is not restricted to the family Gomphonemataceae but seem to be distributed across the entire order Cymbellales. This is shown in this paper for the revived genus Gomphonella, which contains the astigmate group of Gomphoneis and Gomphonema besides the longly disputed G. olivacea. Only a polyphasic approach, combining molecular and micromorphological data for taxonomy, nomenclatural evaluation, and observations from clonal cultures can reveal the full intricacies of evolutionary relations.