Description: Microbial composition and diversity in marine sediments are shaped by environmental, biological, and anthropogenic processes operating at different scales. However, our understanding of benthic microbial biogeography remains limited. Here, we used 16S rDNA amplicon sequencing to characterize benthic microbiota in the North Sea from the top centimeter of 339 sediment samples. We utilized spatially explicit statistical models, to disentangle the effects of the different predictors, including bottom trawling intensity, a prevalent industrial fishing practice which heavily impacts benthic ecosystems. Fitted models demonstrate how the geographic interplay of different environmental and anthropogenic drivers shapes the diversity, structure and potential metabolism of benthic microbial communities. Sediment properties were the primary determinants, with diversity increasing with sediment permeability but also with mud content, highlighting different underlying processes. Additionally, diversity and structure varied with total organic matter content, temperature, bottom shear stress and bottom trawling. Changes in diversity associated with bottom trawling intensity were accompanied by shifts in predicted energy metabolism. Specifically, with increasing trawling intensity, we observed a transition toward more aerobic heterotrophic and less denitrifying predicted metabolism. Our findings provide first insights into benthic microbial biogeographic patterns on a large spatial scale and illustrate how anthropogenic activity such as bottom trawling may influence the distribution and abundances of microbes and potential metabolism at macroecological scales.

Description: 〈jats:title〉Abstract〈/jats:title〉〈jats:p〉Proteomic fingerprinting using MALDI-TOF mass spectrometry is a well-established tool for identifying microorganisms and has shown promising results for identification of animal species, particularly disease vectors and marine organisms. And thus can be a vital tool for biodiversity assessments in ecological studies. However, few studies have tested species identification across different orders and classes. In this study, we collected data from 1246 specimens and 198 species to test species identification in a diverse dataset. We also evaluated different specimen preparation and data processing approaches for machine learning and developed a workflow to optimize classification using random forest. Our results showed high success rates of over 90%, but we also found that the size of the reference library affects classification error. Additionally, we demonstrated the ability of the method to differentiate marine cryptic-species complexes and to distinguish sexes within species.〈/jats:p〉

Description: During the last years DNA barcoding has become a popular method of choice for molecular specimen identification. Here we present a comprehensive DNA barcode library of various crustacean taxa found in the North Sea, one of the most extensively studied marine regions of the world. Our data set includes 1,332 barcodes covering 205 species, including taxa of the Amphipoda, Copepoda, Decapoda, Isopoda, Thecostraca, and others. This dataset represents the most extensive DNA barcode library of the Crustacea in terms of species number to date. By using the Barcode of Life Data Systems (BOLD), unique BINs were identified for 198 (96.6%) of the analyzed species. Six species were characterized by two BINs (2.9%), and three BINs were found for the amphipod species Gammarus salinus Spooner, 1947 (0.4%). Intraspecific distances with values higher than 2.2% were revealed for 13 species (6.3%). Exceptionally high distances of up to 14.87% between two distinct but monophyletic clusters were found for the parasitic copepod Caligus elongatus Nordmann, 1832, supporting the results of previous studies that indicated the existence of an overlooked sea louse species. In contrast to these high distances, haplotype-sharing was observed for two decapod spider crab species, Macropodia parva Van Noort & Adema, 1985 and Macropodia rostrata (Linnaeus, 1761), underlining the need for a taxonomic revision of both species. Summarizing the results, our study confirms the application of DNA barcodes as highly effective identification system for the analyzed marine crustaceans of the North Sea and represents an important milestone for modern biodiversity assessment studies using barcode sequences

Description: Sequence-based specimen identification, known as DNA barcoding, is a common method complementing traditional morphology-based taxonomic assignments. The fundamental resource in DNA barcoding is the availability of a taxonomically reliable sequence database to use as a reference for sequence comparisons. Here, we provide a reference library including 579 sequences of the mitochondrial cytochrome c oxidase subunit I for 113 North Sea mollusc species. We tested the efficacy of this library by simulating a sequence-based specimen identification scenario using Best Match, Best Close Match (BCM) and All Species Barcode (ASB) criteria with three different threshold values. Each identification result was compared with our prior morphology-based taxonomic assignments. Our simulation resulted in 87.7% congruent identifications (93.8% when excluding singletons). The highest number of congruent identifications was obtained with BCM and ASB and a 0.05 threshold. We also compared identifications with genetic clustering (Barcode Index Numbers, BINs) computed by the Barcode of Life Datasystem (BOLD). About 68% of our morphological identifications were congruent with BINs created by BOLD. Forty-nine sequences were clustered in 16 discordant BINs, and these were divided in two classes: sequences from different species clustered in a single BIN and conspecific sequences divided in more BINs. Whereas former incongruences were probably caused by BOLD entries in need of a taxonomic update, the latter incongruences regarded taxa requiring further investigations. These include species with amphi-Atlantic distribution, whose genetic structure should be evaluated over their entire range to produce a reliable sequence-based identification system.

Description: Background: During the last years, the effectiveness of DNA barcoding for animal species identification has been proven in many studies, analyzing both vertebrate and invertebrate taxa. In terms of marine organisms, however, most barcoding studies typically focus on economically relevant species, for example, fish, as well asonthedocumentationof hotspots of species diversity, for example, tropical coral reefs or regions of the almost unexplored deep sea regions. In contrast to this, species diversity of “well-known” habitats is nearly neglected. As part of our running project we started to build up a comprehensive DNA barcode library for the metazoan taxa of the North Sea, one of the most extensively studied ecosystems of the world. The North Sea is characterized by a highamountof anthropogenic pressure such as intensive fishing and ship traffic as well as offshore installations. Environmental parameters (e.g., depth, sediment characteristics, temperature, and salinity) of this semi-enclosed shelf sea follow a distinct pattern: high seasonal fluctuations can be observed in southern areas, but low fluctuations are given in the northern regions. This heterogeneity is also displayed in macrobenthic community structures, with a lower number of species in the shallow southern parts (i.e., the German Bight) and more species in the central and northern North Sea. In addition to this, species with a typical Mediterranean-Lusitanean distribution are also known to occur in parts of the North Sea where oceanic influences prevail. Results: Our barcode library includes a broad variety of taxa, including typical taxa of marine barcoding studies, for example, fish or decapod crustaceans. Our on-growing library also includes groups that are often ignored as cnidarians, parasitic crustaceans, echinoderms, mollusks, pantopods, polychaets, and others. In total, our library includes more than 4200 DNA barcodes of more than 600 species at the moment. By using the Barcode of Life Data Systems (BOLD), unique BINs were identified for more than 90% of the analyzed species. Significance: Our data represent a first step towards the establishment of a comprehensive DNA barcode library of the Metazoa of the North Sea. Despite the fact that various taxa are still missing or are currently underrepresented, our results clearly underline the usefulness of DNA barcodes to discriminate the vast majority of the analyzed species. It should be also kept in mind that the benefits of DNA barcoding are not restricted to taxonomic or systematic research only. The rise of modern high-throughput sequencing technologies will change biomonitoring applications and surveys significantly in the coming years. Following this, reference datasets such as ours will become essential for a correct identification of specimens sequenced as part of a metabarcoding study. This is especially true for the North Sea, a marine region that has been massively affected by cargo ship traffic, the exploitation of oil and gas resources, offshore wind parks, and in particular extensive long-term fisheries.

Description: The Arctic Svalbard Archipelago hosts the world’s northernmost cold-water ‘carbonate factories’ thriving here despite of presumably unfavourable environmental conditions and extreme seasonality. Two contrasting sites of intense biogenic carbonate production, the rhodolith beds in Mosselbukta in the north of the archipelago and the barnacle-mollusc dominated carbonate sediments accumulating in the strong hydrodynamic regime of the Bjørnøy-Banken south of Spitsbergen, were the targets of the RV Maria S. Merian cruise 55 in June 2016. By integrating data from physical oceanography, marine biology, and marine geology, the present contribution characterises the environmental setting and biosedimentary dynamics of these two polar carbonate factories. Repetitive CTD profiling in concert with autonomous temperature/salinity loggers on a long-term settlement platform identified spatiotemporal patterns in the involved Atlantic and Polar water masses, whereas short-term deployments of a lander revealed fluctuations of environmental variables in the rhodolith beds in Mosselbukta and at same depth (46 m) at Bjørnøy-Banken. At both sites, dissolved inorganic nutrients in the water column were found depleted (except for elevated ammonium concentrations) and show an overall increase in concentration and N:P ratios toward deeper waters. This indicates that a recycling system was fuelling primary production after the phytoplankton spring bloom at the time of sampling in June 2016. Accordingly, oxygen levels were found elevated and carbon dioxide concentrations (pCO2) markedly reduced, on average only half the expected equilibrium values. Backed up by seawater stable carbon and oxygen isotope signatures, this is interpreted as an effect of limited air-sea gas exchange during seasonal ice cover in combination with a boost in community photosynthesis during the spring phytoplankton bloom. The observed trends are enhanced by the onset of rhodophyte photosynthesis in the rhodolith beds during the polar day upon retreat of sea-ice. Potential adverse effects of ocean acidification on the local calcifier community are thus predicted to be seasonally buffered by the marked drop in pCO2 during the phase of sea-ice cover and spring phyto-plankton bloom, but this effect will diminish should the seasonal sea-ice formation continue to decline. Among the 25 macrobenthos taxa identified from images captured by the lander’s camera system, all but three species were calcifiers contributing to the carbonate production. Biodiversity was found to be much higher in Mosselbukta (21 taxa) compared to Bjørnøy-Banken (8 taxa), which is considered as a result of enhanced habitat diversity provided in the rhodolith beds by the bioengineering crustose alga Lithothamnion glaciale. Filter-feeding activity of selected key species did reveal group-specific but no common activity patterns. Biotic disturbance of the filtering activity was common, in contrast to abiotic factors, with hermit crabs representing the primary trigger. Motion tracking of rhodoliths revealed a high frequency of dislocation, triggered not by abiotic factors but by the activity of benthic invertebrates, in particular echinoids ploughing below or moving over the rhodoliths. The echinoid Strongylocentrotus sp. is the most abundant component of the associated fauna, thereby considerably contributing both to carbonate production and to grazing bioerosion. Together, these results portray a high degree of seasonal as well as short-term dynamics in environmental conditions that despite many similarities support distinctly different communities and biodiversity patterns in the calcifying macrobenthos at the two studied polar carbonate factories.