Einschätzen phylogenetischer Abgrenzungen von Taxa fademförmiger Xanthophyceae (Stramenopiles) mithilfe von DNA Sequenzanalysen und Morphologie

This thesis focuses on assessing taxonomic boundaries among the filamentous members of “yellow-green algae”, i.e. the class Xanthophyceae (Stramenopiles), which are widespread microalgae in freshwater or terrestrial habitats. The scarcity of morphological characters as well as their considerable plasticity requires the employment of molecular marker sequences to define monophyletic genera and species as well as for the unambiguous identification of new isolates. The genetic diversity and species boundaries within genera of Tribonemataceae, i.e Xanthonema Silva, Bumilleria Borzì, Bumilleriopsis Printz, Pseudobumilleriopsis Deason & Bold and Tribonema Derbès & Solier, were assessed using the highly variable psbA/rbcL spacer region as well as the more conserved full rbcL gene sequences. A method and a reference data base for the unambiguous identification of species of Heterococcus Chodat which uses DNA sequence variation in markers from plastid and nuclear genomes were established. In all studied cases the molecular-based species boundaries were more conservative than those defined by morphology. Within a single species almost identical genotypes were repeatedly recovered from strains of different geographic origins. However, the genotypes recovered from Antarctic strains were distinct from those of temperate regions.Die vorliegende Arbeit hat zum Ziel taxonomische Abgrenzungen bei fadenförmigen „Gelbgrünalgen“, d.h. Vertretern der Klasse Xanthophyceae (Stramenopiles), festzustellen. Fadenförmige Xanthophyceae sind weitverbreitete Mikroalgen im Süßwasser und in terrestrischen Lebensräumen. Da diese Algen arm an morphologischen Merkmalen sind und diese zudem eine beträchtliche Plastizität aufweisen, ist es notwendig, molekulare Markersequenzen einzusetzen, um monophyletische Gattungen und Arten zu definieren und neue Isolate auf Artniveau eindeutig bestimmen zu können. Die genetische Diversität und die Abgrenzungen von Gattungen der Tribonemataceae, d.h. Xanthonema Silva, Bumilleria Borzì, Bumilleriopsis Printz, Pseudobumilleriopsis Deason & Bold und Tribonema Derbès & Solier, wurden anhand hochvariabler Sequencen der psbA/rbcL Spacer-Region als auch konservierterer vollständigr rbcL Gensequenzen erfasst. Zur eindeutigen Identifizierung von Arten der Gattung Heterococcus Chodat wurden eine neue Methode und Referenzdaten erarbeitet, die auf Sequenzvariationen in Markermolekülen sowohl des Plastiden- als auch des Kerngenoms beruhen. In allen untersuchten Fällen waren die molekular-phylogenetisch begründeten Artabgrenzungen konservativer als die aufgrund morphologischer Merkmale. Innerhalb derselben Art wurden wiederholt nahezu identische Genotypen, die aber aus verschiedenen geographischen Ursprüngen stammten, aufgedeckt. Jedoch waren die Genotypen der Stämme, die aus der Antarktis isoliert wurden, verschieden von denen aus anderen temperaten geographischen Regionen

Congruence of chloroplast- and nuclear-encoded DNA sequence variations used to assess species boundaries in the soil microalga Heterococcus (Stramenopiles, Xanthophyceae).

BackgroundHeterococcus is a microalgal genus of Xanthophyceae (Stramenopiles) that is common and widespread in soils, especially from cold regions. Species are characterized by extensively branched filaments produced when grown on agarized culture medium. Despite the large number of species described exclusively using light microscopic morphology, the assessment of species diversity is hampered by extensive morphological plasticity.ResultsTwo independent types of molecular data, the chloroplast-encoded psbA/rbcL spacer complemented by rbcL gene and the internal transcribed spacer 2 of the nuclear rDNA cistron (ITS2), congruently recovered a robust phylogenetic structure. With ITS2 considerable sequence and secondary structure divergence existed among the eight species, but a combined sequence and secondary structure phylogenetic analysis confined to helix II of ITS2 corroborated relationships as inferred from the rbcL gene phylogeny. Intra-genomic divergence of ITS2 sequences was revealed in many strains. The 'monophyletic species concept', appropriate for microalgae without known sexual reproduction, revealed eight different species. Species boundaries established using the molecular-based monophyletic species concept were more conservative than the traditional morphological species concept. Within a species, almost identical chloroplast marker sequences (genotypes) were repeatedly recovered from strains of different origins. At least two species had widespread geographical distributions; however, within a given species, genotypes recovered from Antarctic strains were distinct from those in temperate habitats. Furthermore, the sequence diversity may correspond to adaptation to different types of habitats or climates.ConclusionsWe established a method and a reference data base for the unambiguous identification of species of the common soil microalgal genus Heterococcus which uses DNA sequence variation in markers from plastid and nuclear genomes. The molecular data were more reliable and more conservative than morphological data

Invading grass-like alga transforms rippled sand bars into bumpy muddy flats: arrival of a game changer in the Wadden Sea

In the wake of biological globalization, translocated species of high bio-engineering capacity increasingly change bottom topography of sedimentary coasts. A Vaucheria-taxon (Xanthophyceae) of unknown origin is spreading at the transition between intertidal and subtidal zones, while resident Vaucheria-species are confined to the upper shore in the Wadden Sea (European Atlantic). Near the island of Sylt, dense turfs of green filaments rapidly expanded over an area of 180 ha within 3 years. The unicellular filaments reach about 5 cm out of and 5 cm into the sediment. Felted rhizoids provide firm anchorage. Dry phytomass (up to 208 g m-2) was similar to that of intertidal seagrass beds. Residual filaments overwinter in the sediment and give rise to renewed growth in late spring. In addition, oospores germinate. Fine particles are trapped by the turf during summer, generating laminated cohesive mud. Muddy hummocks arise up to 20 cm above ambient sand flats, alternating with troughs but gradually merge into coherent and pertinacious plateaus of mud. This shift in bottom topography and sediment composition may potentially change the mud balance of tidal basins, and the capacity of tidal flats in catching up with accelerating sea-level rise

Unrecognized diversity and distribution of soil algae from Maritime Antarctica (Fildes Peninsula, King George Island)

IntroductionEukaryotic algae in the top few centimeters of fellfield soils of ice-free Maritime Antarctica have many important effects on their habitat, such as being significant drivers of organic matter input into the soils and reducing the impact of wind erosion by soil aggregate formation. To better understand the diversity and distribution of Antarctic terrestrial algae, we performed a pilot study on the surface soils of Meseta, an ice-free plateau mountain crest of Fildes Peninsula, King George Island, being hardly influenced by the marine realm and anthropogenic disturbances. It is openly exposed to microbial colonization from outside Antarctica and connected to the much harsher and dryer ice-free zones of the continental Antarctic. A temperate reference site under mild land use, SchF, was included to further test for the Meseta algae distribution in a contrasting environment.MethodsWe employed a paired-end metabarcoding analysis based on amplicons of the highly variable nuclear-encoded ITS2 rDNA region, complemented by a clone library approach. It targeted the four algal classes, Chlorophyceae, Trebouxiophyceae, Ulvophyceae, and Xanthophyceae, representing key groups of cold-adapted soil algae.ResultsA surprisingly high diversity of 830 algal OTUs was revealed, assigned to 58 genera in the four targeted algal classes. Members of the green algal class Trebouxiophyceae predominated in the soil algae communities. The major part of the algal biodiversity, 86.1% of all algal OTUs, could not be identified at the species level due to insufficient representation in reference sequence databases. The classes Ulvophyceae and Xanthophyceae exhibited the most unknown species diversity. About 9% of the Meseta algae species diversity was shared with that of the temperate reference site in Germany.DiscussionIn the small portion of algal OTUs for which their distribution could be assessed, the entire ITS2 sequence identity with references shows that the soil algae likely have a wide distribution beyond the Polar regions. They probably originated from soil algae propagule banks in far southern regions, transported by aeolian transport over long distances. The dynamics and severity of environmental conditions at the soil surface, determined by high wind currents, and the soil algae’s high adaptability to harsh environmental conditions may account for the high similarity of soil algal communities between the northern and southern parts of the Meseta

Repositories for Taxonomic Data: Where We Are and What is Missing

AbstractNatural history collections are leading successful large-scale projects of specimen digitization (images, metadata, DNA barcodes), thereby transforming taxonomy into a big data science. Yet, little effort has been directed towards safeguarding and subsequently mobilizing the considerable amount of original data generated during the process of naming 15,000–20,000 species every year. From the perspective of alpha-taxonomists, we provide a review of the properties and diversity of taxonomic data, assess their volume and use, and establish criteria for optimizing data repositories. We surveyed 4113 alpha-taxonomic studies in representative journals for 2002, 2010, and 2018, and found an increasing yet comparatively limited use of molecular data in species diagnosis and description. In 2018, of the 2661 papers published in specialized taxonomic journals, molecular data were widely used in mycology (94%), regularly in vertebrates (53%), but rarely in botany (15%) and entomology (10%). Images play an important role in taxonomic research on all taxa, with photographs used in &amp;gt;80% and drawings in 58% of the surveyed papers. The use of omics (high-throughput) approaches or 3D documentation is still rare. Improved archiving strategies for metabarcoding consensus reads, genome and transcriptome assemblies, and chemical and metabolomic data could help to mobilize the wealth of high-throughput data for alpha-taxonomy. Because long-term—ideally perpetual—data storage is of particular importance for taxonomy, energy footprint reduction via less storage-demanding formats is a priority if their information content suffices for the purpose of taxonomic studies. Whereas taxonomic assignments are quasifacts for most biological disciplines, they remain hypotheses pertaining to evolutionary relatedness of individuals for alpha-taxonomy. For this reason, an improved reuse of taxonomic data, including machine-learning-based species identification and delimitation pipelines, requires a cyberspecimen approach—linking data via unique specimen identifiers, and thereby making them findable, accessible, interoperable, and reusable for taxonomic research. This poses both qualitative challenges to adapt the existing infrastructure of data centers to a specimen-centered concept and quantitative challenges to host and connect an estimated $\le$2 million images produced per year by alpha-taxonomic studies, plus many millions of images from digitization campaigns. Of the 30,000–40,000 taxonomists globally, many are thought to be nonprofessionals, and capturing the data for online storage and reuse therefore requires low-complexity submission workflows and cost-free repository use. Expert taxonomists are the main stakeholders able to identify and formalize the needs of the discipline; their expertise is needed to implement the envisioned virtual collections of cyberspecimens. [Big data; cyberspecimen; new species; omics; repositories; specimen identifier; taxonomy; taxonomic data.]</jats:p

Congruence of chloroplast- and nuclear-encoded DNA sequence variations used to assess species boundaries in the soil microalga Heterococcus (Stramenopiles, Xanthophyceae).

BackgroundHeterococcus is a microalgal genus of Xanthophyceae (Stramenopiles) that is common and widespread in soils, especially from cold regions. Species are characterized by extensively branched filaments produced when grown on agarized culture medium. Despite the large number of species described exclusively using light microscopic morphology, the assessment of species diversity is hampered by extensive morphological plasticity.ResultsTwo independent types of molecular data, the chloroplast-encoded psbA/rbcL spacer complemented by rbcL gene and the internal transcribed spacer 2 of the nuclear rDNA cistron (ITS2), congruently recovered a robust phylogenetic structure. With ITS2 considerable sequence and secondary structure divergence existed among the eight species, but a combined sequence and secondary structure phylogenetic analysis confined to helix II of ITS2 corroborated relationships as inferred from the rbcL gene phylogeny. Intra-genomic divergence of ITS2 sequences was revealed in many strains. The 'monophyletic species concept', appropriate for microalgae without known sexual reproduction, revealed eight different species. Species boundaries established using the molecular-based monophyletic species concept were more conservative than the traditional morphological species concept. Within a species, almost identical chloroplast marker sequences (genotypes) were repeatedly recovered from strains of different origins. At least two species had widespread geographical distributions; however, within a given species, genotypes recovered from Antarctic strains were distinct from those in temperate habitats. Furthermore, the sequence diversity may correspond to adaptation to different types of habitats or climates.ConclusionsWe established a method and a reference data base for the unambiguous identification of species of the common soil microalgal genus Heterococcus which uses DNA sequence variation in markers from plastid and nuclear genomes. The molecular data were more reliable and more conservative than morphological data

Biotechnological Screening of Microalgal and Cyanobacterial Strains for Biogas Production and Antibacterial and Antifungal Effects

Microalgae and cyanobacteria represent a valuable natural resource for the generation of a large variety of chemical substances that are of interest for medical research, can be used as additives in cosmetics and food production, or as an energy source in biogas plants. The variety of potential agents and the use of microalgae and cyanobacteria biomass for the production of these substances are little investigated and not exploited for the market. Due to the enormous biodiversity of microalgae and cyanobacteria, they hold great promise for novel products. In this study, we investigated a large number of microalgal and cyanobacterial strains from the Culture Collection of Algae at Göttingen University (SAG) with regard to their biomass and biogas production, as well antibacterial and antifungal effects. Our results demonstrated that microalgae and cyanobacteria are able to generate a large number of economically-interesting substances in different quantities dependent on strain type. The distribution and quantity of some of these components were found to reflect phylogenetic relationships at the level of classes. In addition, between closely related species and even among multiple isolates of the same species, the productivity may be rather variable

Invasive Vaucheria (Xanthophyceae) at the lower shore of the Wadden Sea

Vaucheria species have previously been restricted to upper shore habitats in the Wadden Sea (eastern North Sea, European Atlantic). In contrast to these previous observations, we have now found Vaucheria longicaulis and a distinct plastid lineage of V. velutina spreading along the lower shores, forming extensive turfs at and below low tide level under fully marine conditions near the Island of Sylt. Species and populations were identified by morphological features and reconfirmed by sequencing the plastid-encoding gene rbcL and the psbA-rbcL spacer region. We needed to modify primer sequences to successfully amplify the rbcL region of marine and brackish Vaucheria species. Due to distinct phylogenetic grouping, we can reject the possibility of niche expansions from the upper shore and propose recent introductions as the cause of the newly formed populations at the lower shore

Data storage and data re-use in taxonomy-the need for improved storage and accessibility of heterogeneous data

Gemeinholzer B, Vences M, Beszteri B, et al. Data storage and data re-use in taxonomy-the need for improved storage and accessibility of heterogeneous data. ORGANISMS DIVERSITY &amp; EVOLUTION. 2020;20(1):1-8.The ability to rapidly generate and share molecular, visual, and acoustic data, and to compare them with existing information, and thereby to detect and name biological entities is fundamentally changing our understanding of evolutionary relationships among organisms and is also impacting taxonomy. Harnessing taxonomic data for rapid, automated species identification by machine learning tools or DNA metabarcoding techniques has great potential but will require their review, accessible storage, comprehensive comparison, and integration with prior knowledge and information. Currently, data production, management, and sharing in taxonomic studies are not keeping pace with these needs. Indeed, a survey of recent taxonomic publications provides evidence that few species descriptions in zoology and botany incorporate DNA sequence data. The use of modern high-throughput (-omics) data is so far the exception in alpha-taxonomy, although they are easily stored in GenBank and similar databases. By contrast, for the more routinely used image data, the problem is that they are rarely made available in openly accessible repositories. Improved sharing and re-using of both types of data requires institutions that maintain long-term data storage and capacity with workable, user-friendly but highly automated pipelines. Top priority should be given to standardization and pipeline development for the easy submission and storage of machine-readable data (e.g., images, audio files, videos, tables of measurements). The taxonomic community in Germany and the German Federation for Biological Data are researching options for a higher level of automation, improved linking among data submission and storage platforms, and for making existing taxonomic information more readily accessible

Crustal structure of the Mendeleev Rise and the Chukchi Plateau (Arctic Ocean) along the Russian wide-angle and multichannel seismic reflection experiment “Arctic-2012”

We present a seismic and density model for the crust and the uppermost mantle of the Arctic Ocean off-shore Chukotka down to a 40 km depth along a 740-km long latitudinal (at ca. 77°N) “Arctic-2012” wide-angle/MCS profile. Joint seismic and gravity modeling indicates significant differences in the crustal velocity and density structure of the northeastern Vilkitsky Trough, the Mendeleev Rise, the Chukchi Basin, and the Chukchi Plateau. The Vilkitsky Trough and the Chukchi Basin have a thin crust (23 km and 18 km, correspondingly), 6–8 km thick sedimentary cover, 3–6 km thick upper/middle crust (with the smallest thickness of 3–4 km beneath the Chukchi Basin), and 9–10 km thick lower crust. The uppermost mantle of the Chukchi Basin has a high density (3.27–3.31 g/cm3) and a low velocity (Vp ∼ 7.8 km/s), which we explain by 5–10% serpentinization of mantle peridotite at a 22–35 km depth as a result of crustal hyperextension and seawater penetration. The Chukchi Plateau and the Mendeleev Rise have a thick crust (28–29 km and 33–34 km, correspondingly), underlain by a normal mantle (Vp ∼ 8.0 km/s). The Chukchi Plateau has a 2‐4 km thick sedimentary cover, a thick (15–18 km) upper/middle crust with low-Vp, low-density lenses interpreted as magmatic intrusions, and a 9–12 km thick lower crust. The Mendeleev Rise has a 3–7 km thick sedimentary cover (most of which is formed by metasediments with a possible presence of volcanic rocks), a 7–8 km thick upper/middle crust, and a thick (20 km) lower crust which includes a 3–4 km thick high-velocity (Vp ∼ 7.3 km/s) underplated magmatic material. The high density anomaly (at depths >35 km) below the Mendeleev Rise is interpreted as an eclogitic body in the upper mantle lithosphere. Seismic Vp and Vp/Vs structure of the crust along the “Arctic-2012” profile indicates its continental nature: a 3–18 km thick upper/middle crustal layer with Vp ∼ 6.0–6.8 km/s and Vp/Vs ∼ 1.70–1.73 typical of felsic-intermediate continental upper crust is present along the entire profile. Strong variability of the crustal structure along the profile reflects its significant modification by metamorphism and magmatism, possibly related to the High-Arctic Large Igneous Province and localized lithosphere extension beneath the Chukchi Basin