Epilithic diatom communities of selected streams from the Lerma-Chapala Basin, Central Mexico, with the description of two new species

The Lerma-Chapala Basin, in Central Mexico, is geologically heterogeneous, climatically diverse and boasts high biodiversity, lying within two Biodiversity Hotspots, namely Mesoamerica and the Madrean Pine–Oak Woodlands. Epilithon and water samples were collected in the basin from 14 sampling sites three times each, two sampling campaigns during the rainy season and one in the dry season. A total of 274 infrageneric taxa in 48 genera were recorded. The taxonomic composition observed was dominated by taxa from the genera Nitzschia, Gomphonema, Pinnularia, Navicula, Sellaphora and Eunotia. About a third of the taxa found could not be identified to the species level. From those unidentified morphodemes, two are described as new species, namely Brachysira altepetlensis and Sellaphora queretana. Furthermore, Eolimna rhombica is transferred to Sellaphora. Canonical Correspondence Analysis (CCA) revealed that specific conductivity and pH were the main environmental factors driving the community composition observed. Three groups of samples were identified after the CCA: 1) characterized by acidic waters and low conductivity; 2) with circumneutral waters, low specific conductivity and high temperature and phosphorous concentrations; and 3) characterized by circumneutral waters, high conductivity and low nitrogen concentrations. The indicator value method (IndVal), based on the relative abundance and relative frequency of the most abundant taxa was calculated based on the groups observed in the CCA, identifying the characteristic taxa for each of the three groups

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

Exploring diatom diversity through cultures - a case study from the Bow River, Canada

Diatom cultures can help answer taxonomic, biogeographic and ecological questions on a local and global scale. Unialgal cultures are derived from a single cell and provide abundant material for morphological and molecular analyses. The link between the historic morphological species concept and the molecular data is becoming increasingly important with the use of eDNA metabarcoding. Additionally, cultures provide insights into the life cycle of diatoms and thereby complement taxonomy and species ecology. In this study, we present an approach to extract benthic diatoms from an environmental sample to generate unialgal cultures. We explored diatom diversity in preserved assemblages and by culturing as many different taxa as possible from benthic freshwater samples taken on the same day from the Bow River in Calgary, Canada. With both methods we found a total of 221 different benthic diatom taxa, of which 182 were identified in the preserved diatom assemblages. Interestingly, an additional 39 taxa only appeared in the cultures. In total 129 strains were cultivated representing 71 different taxa. This study includes pictures of living cells demonstrating the additional merits of unialgal cultures, as they provide information on plastid details, auxospores and endosymbionts. Both, the identification of the diatom assemblages and the generation and identification of strains provide the foundation for additional water quality assessment tools, taxonomic insights and molecular references libraries

Exploring benthic diatom diversity in the West Antarctic Peninsula: insights from a morphological and molecular approach

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

Contributions to the biodiversity of Vietnam – Results of VIETBIO inventory work and field training in Cuc Phuong National Park

VIETBIO [Innovative approaches to biodiversity discovery and characterisation in Vietnam] is a bilateral German-Vietnamese research and capacity building project focusing on the development and transfer of new methods and technology towards an integrated biodiversity discovery and monitoring system for Vietnam. Dedicated field training and testing of innovative methodologies were undertaken in Cuc Phuong National Park as part and with support of the project, which led to the new biodiversity data and records made available in this article collection. VIETBIO is a collaboration between the Museum für Naturkunde Berlin – Leibniz Institute for Evolution and Biodiversity Science (MfN), the Botanic Garden and Botanical Museum, Freie Universität Berlin (BGBM) and the Vietnam National Museum of Nature (VNMN), the Institute of Ecology and Biological Resources (IEBR), the Southern Institute of Ecology (SIE), as well as the Institute of Tropical Biology (ITB); all Vietnamese institutions belong to the Vietnam Academy of Science and Technology (VAST). The article collection "VIETBIO" (https://doi.org/10.3897/bdj.coll.63) reports original results of recent biodiversity recording and survey work undertaken in Cuc Phuong National Park, northern Vietnam, under the framework of the VIETBIO project. The collection consist of this “main” cover paper – characterising the study area, the general project approaches and activities, while also giving an extensive overview on previous studies from this area – followed by individual papers for higher taxa as studied during the project. The main purpose is to make primary biodiversity records openly available, including several new and interesting findings for this biodiversity-rich conservation area. All individual data papers with their respective primary records are expected to provide useful baselines for further taxonomic, phylogenetic, ecological and conservation-related studies on the respective taxa and, thus, will be maintained as separate datasets, including separate GUIDs also for further updating

Evaluating the ecological status of mountain streams from a megacity (Mexico City) with diatoms: development and implementation of morphological and eDNA-based methods

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

Does the Cosmopolitan Diatom <i>Gomphonema parvulum</i> (Kützing) Kützing Have a Biogeography?

<div><p>Diatom cultures of the <i>G. parvulum</i> 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 <i>G. parvulum</i> (Kützing) Kützing sensu lato: its nominate variety (var. <i>parvulum</i>), <i>G. parvulum</i> var. <i>exilissimum</i> Grunow and <i>G. parvulum</i> f. <i>saprophilum</i> Lange-Bertalot & Reichardt, <i>G. [parvulum</i> var.] <i>lagenula</i> Kützing plus four unidentifiable morphodemes. The concatenated analysis of the sequences of the markers 18SV4, <i>rbc</i>L, 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, <i>G. parvulum sensu stricto</i>, and <i>G. lagenula</i>, were emended, G. <i>saprophilum</i> elevated to species rank and epitypes designated. One species was newly described.</p></div

LM photos of strains.

<p>Figs. 2.1–22. <i>Gomphonema parvulum</i> (Kützing) Kützing var. <i>parvulum</i>. Figs. 2.1–3. Strain D16_042, Figs. 2.4–6. Strain D16_044, Fig. 2.7. Strain D16_005, Fig. 2.8. Strain D16_009, Figs. 2.9–11. Strain D16_008, Figs. 2.12–15. Strain D16_004, Figs. 2.16–18. EPITYPE Strain D16_045. Figs. 2.19–20. Strain D13_034, Fig. 2.21. Strain D16_030, Fig. 2.22. Strain D16_027. Figs. 2.23. Strain D16_026, <i>Gomphonema parvulum</i> var. nov.? Figs. 2.24–25. Strain D12_022, <i>Gomphonema parvulum</i> var. <i>parvulum</i> [morphodeme exilissimum]. Figs. 2.26–28. <i>Gomphonema lagenula</i> Kützing. Figs. 2.26–27. Strain D33_006. Fig. 2.28. EPITYPE Strain D33_024. Figs. 2.29–34. <i>Gomphonema parvulum</i> var. nov.? Figs. 2.29. Strain D16_028. Figs. 2.30–34. Strain D16_011. Figs. 2.35–43. <i>Gomphonema saprophilum</i> (Lange-Bertalot & Reichardt) Abarca et al. comb. nov. Figs. 2.35–38. EPITYPE Strain D36_003. Figs. 2.39–41. Strain D20_027, Figs. 2.42–43. Strain D03_167. Figs. 2.44–49. <i>Gomphonema narodoense</i> R. Jahn et al. sp. nov. Figs. 2.44–46. HOLOTYPE Strain D23_012. Figs. 2.46–49. Strain D23_009. Scale bars represent 10 µm.</p

Strict consensus tree of the ML analysis of the combined dataset (molecular markers 18SV4, internal transcribed spacer ITS, and <i>rbc</i>L) including Genbank sequences with the results of the SAMS analysis (arrows), bootstrap values (>75) of MP (PB) and ML (LB) as well as Bayesian posterior probabilities (PP) (>0.75).

<p>Split names indicate the splits from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086885#pone-0086885-g007" target="_blank">Fig. 7</a>.</p