Senckenberg am Meer

This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re-introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under-sampled areas and from environmental genomic information.

This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users.

Abstract. The deep sea, the largest biome on Earth, has a series of characteristics that make this environment both distinct from other marine and land ecosystems and unique for the entire planet. This review describes these patterns and processes, from geological settings to biological processes, biodiversity and biogeographical patterns. It concludes with a brief discussion of current threats from anthropogenic activities to deep-sea habitats and their fauna. Investigations of deep-sea habitats and their fauna began in the late 19th century. In the intervening years, technological developments and stimulating discoveries have promoted deep-sea research and changed our way of understanding life on the planet. Nevertheless, the deep sea is still mostly unknown and current discovery rates of both habitats and species remain high. The geological, physical and geochemical settings of the deep-sea floor and the water column form a series of different habitats with unique characteristics that support specific faunal communities. Since 1840, 28 new habitats/ecosystems have been discovered from the shelf break to the deep trenches and discoveries of new habitats are still happening in the early 21st century. However, for most of these habitats the global area covered is unknown or has been only very roughly estimated; an even smaller – indeed, minimal – proportion has actually been sampled and investigated. We currently perceive most of the deep-sea ecosystems as heterotrophic, depending ultimately on the flux on organic matter produced in the overlying surface ocean through photosynthesis. The resulting strong food limitation thus shapes deep-sea biota and communities, with exceptions only in reducing ecosystems such as inter alia hydrothermal vents or cold seeps. Here, chemoautolithotrophic bacteria play the role of primary producers fuelled by chemical energy sources rather than sunlight. Other ecosystems, such as seamounts, canyons or cold-water corals have an increased productivity through specific physical processes, such as topographic modification of currents and enhanced transport of particles and detrital matter. Because of its unique abiotic attributes, the deep sea hosts a specialized fauna. Although there are no phyla unique to deep waters, at lower taxonomic levels the composition of the fauna is distinct from that found in the upper ocean. Amongst other characteristic patterns, deep-sea species may exhibit either gigantism or dwarfism, related to the decrease in food availability with depth. Food limitation on the seafloor and water column is also reflected in the trophic structure of heterotrophic deep-sea communities, which are adapted to low energy availability. In most of these heterotrophic habitats, the dominant megafauna is composed of detritivores, while filter feeders are abundant in habitats with hard substrata (e.g. mid-ocean ridges, seamounts, canyon walls and coral reefs). Chemoautotrophy through symbiotic relationships is dominant in reducing habitats. Deep-sea biodiversity is among of the highest on the planet, mainly composed of macro and meiofauna, with high evenness. This is true for most of the continental margins and abyssal plains with hot spots of diversity such as seamounts or cold-water corals. However, in some ecosystems with particularly "extreme" physicochemical processes (e.g. hydrothermal vents), biodiversity is low but abundance and biomass are high and the communities are dominated by a few species. Two large-scale diversity patterns have been discussed for deep-sea benthic communities. First, a unimodal relationship between diversity and depth is observed, with a peak at intermediate depths (2000–3000 m), although this is not universal and particular abiotic processes can modify the trend. Secondly, a poleward trend of decreasing diversity has been discussed, but this remains controversial and studies with larger and more robust data sets are needed. Because of the paucity in our knowledge of habitat coverage and species composition, biogeographic studies are mostly based on regional data or on specific taxonomic groups. Recently, global biogeographic provinces for the pelagic and benthic deep ocean have been described, using environmental and, where data were available, taxonomic information. This classification described 30 pelagic provinces and 38 benthic provinces divided into 4 depth ranges, as well as 10 hydrothermal vent provinces. One of the major issues faced by deep-sea biodiversity and biogeographical studies is related to the high number of species new to science that are collected regularly, together with the slow description rates for these new species. Taxonomic coordination at the global scale is particularly difficult, but is essential if we are to analyse large diversity and biogeographic trends.

Ripple, flaser and lenticular bedding are well known, but for describing profiles, they are not sufficiently defined and subdivided. It is, therefore, the intent of the following text to present such a definition and classification. The classification contains the following main bedding types and intermediary types (Fig.1): 1 Cross-bedding with flasers. 2 Flaser bedding, subdivided in: (a) simple flaser bedding; (b) bifurcated flaser bedding; (c) wavy flaser bedding; (d) bifurcated wavy flaser bedding. 3 Wavy bedding. 4 Lenticular bedding with thick or flat lenses, subdivided in: (a) continuous lenticular bedding (with connected lenses); (b) broken lenticular bedding (with single lenses).

A total of 19 honey samples, mostly from Germany but also from France, Italy, Spain and Mexico, were analysed for non-pollen particulates. Only coloured fibres and fragments were quantified. Transparent fibres, considered to be cellulosic because they could be stained with fuchsin, were not quantified. Coloured material was found in all the samples investigated. Fibre counts ranged from 40/kg to 660/kg of honey, with a mean value of 166 ± 147/kg of honey, whereas fragments were considerably less abundant (0-38/kg of honey; mean 9 ± 9/kg of honey). Sources are tentatively identified as environmental, that is particles having been transported by the bees into the hive, or having been introduced during honey processing or both. In addition, five commercial sugars were analysed. In all the refined samples, transparent and coloured fibres (mean 217 ± 123/kg of sugar) and fragments (32 ± 7/kg of sugar) were found. Unrefined cane sugar had 560 fibres and 540 fragments per kilogram of honey. In addition, in both honey and sugar samples, granular non-pollen material was observed.

Local biodiversity trends over time are likely to be decoupled from global trends, as local processes may compensate or counteract global change. We analyze 161 long-term biological time series (15-91 years) collected across Europe, using a comprehensive dataset comprising ~6,200 marine, freshwater and terrestrial taxa. We test whether (i) local long-term biodiversity trends are consistent among biogeoregions, realms and taxonomic groups, and (ii) changes in biodiversity correlate with regional climate and local conditions. Our results reveal that local trends of abundance, richness and diversity differ among biogeoregions, realms and taxonomic groups, demonstrating that biodiversity changes at local scale are often complex and cannot be easily generalized. However, we find increases in richness and abundance with increasing temperature and naturalness as well as a clear spatial pattern in changes in community composition (i.e. temporal taxonomic turnover) in most biogeoregions of Northern and Eastern Europe.

Molecular tools have revolutionized the exploration of biodiversity, especially in organisms for which traditional taxonomy is difficult, such as for microscopic animals (meiofauna). Environmental (eDNA) metabarcode surveys of DNA extracted from sediment samples are increasingly popular for surveying biodiversity. Most eDNA surveys use the nuclear gene-encoding small-subunit rDNA gene (18S) as a marker; however, different markers and metrics used for delimiting species have not yet been evaluated against each other or against morphologically defined species (morphospecies). We assessed more than 12,000 meiofaunal sequences of 18S and of the main alternatively used marker [Cytochrome c oxidase subunit I (COI) mtDNA] belonging to 55 datasets covering three taxonomic ranks. Our results show that 18S reduced diversity estimates by a factor of 0.4 relative to morphospecies, whereas COI increased diversity estimates by a factor of 7.6. Moreover, estimates of species richness using COI were robust among three of four commonly used delimitation metrics, whereas estimates using 18S varied widely with the different metrics. We show that meiofaunal diversity has been greatly underestimated by 18S eDNA surveys and that the use of COI provides a better estimate of diversity. The suitability of COI is supported by cross-mating experiments in the literature and evolutionary analyses of discreteness in patterns of genetic variation. Furthermore its splitting of morphospecies is expected from documented levels of cryptic taxa in exemplar meiofauna. We recommend against using 18S as a marker for biodiversity surveys and suggest that use of COI for eDNA surveys could provide more accurate estimates of species richness in the future.

Commercial-scale mining for polymetallic nodules could have a major impact on the deep-sea environment, but the effects of these mining activities on deep-sea ecosystems are very poorly known. The first commercial test mining for polymetallic nodules was carried out in 1970. Since then a number of small-scale commercial test mining or scientific disturbance studies have been carried out. Here we evaluate changes in faunal densities and diversity of benthic communities measured in response to these 11 simulated or test nodule mining disturbances using meta-analysis techniques. We find that impacts are often severe immediately after mining, with major negative changes in density and diversity of most groups occurring. However, in some cases, the mobile fauna and small-sized fauna experienced less negative impacts over the longer term. At seven sites in the Pacific, multiple surveys assessed recovery in fauna over periods of up to 26 years. Almost all studies show some recovery in faunal density and diversity for meiofauna and mobile megafauna, often within one year. However, very few faunal groups return to baseline or control conditions after two decades. The effects of polymetallic nodule mining are likely to be long term. Our analyses show considerable negative biological effects of seafloor nodule mining, even at the small scale of test mining experiments, although there is variation in sensitivity amongst organisms of different sizes and functional groups, which have important implications for ecosystem responses. Unfortunately, many past studies have limitations that reduce their effectiveness in determining responses. We provide recommendations to improve future mining impact test studies. Further research to assess the effects of test-mining activities will inform ways to improve mining practices and guide effective environmental management of mining activities.

Polymetallic nodule mining at abyssal depths in the Clarion Clipperton Fracture Zone (Eastern Central Pacific) will impact one of the most remote and least known environments on Earth. Since vast areas are being targeted by concession holders for future mining, large-scale effects of these activities are expected. Hence, insight into the fauna associated with nodules is crucial to support effective environmental management. In this study video surveys were used to compare the epifauna from sites with contrasting nodule coverage in four license areas. Results showed that epifaunal densities are more than two times higher at dense nodule coverage (>25 versus ≤10 individuals per 100 m(2)), and that taxa such as alcyonacean and antipatharian corals are virtually absent from nodule-free areas. Furthermore, surveys conducted along tracks from trawling or experimental mining simulations up to 37 years old, suggest that the removal of epifauna is almost complete and that its full recovery is slow. By highlighting the importance of nodules for the epifaunal biodiversity of this abyssal area, we urge for cautious consideration of the criteria for determining future preservation zones.

Analyzing one of the most extensive long‐term data series in the North Sea, the Helgoland Roads time series, we investigated the changes in the factors that potentially drive phytoplankton bloom dynamics in the German Bight. We compared the changes in these factors with the changes in the spring bloom phenology. We combined zooplankton, nutrient, weather, and phytoplankton data to analyze whether there has been a shift in trophic interactions in the North Sea affecting the spring bloom timing. The potential influence of temperature, with a mean increase of 1.5°C, was investigated. We showed that the German Bight around Helgoland is a highly dynamic system and has undergone considerable change in the last 30 yr. Nutrient levels, temperature, underwater light climate and wind speed have all changed. However, the spring bloom dynamics have hardly changed at all. We showed that the spring bloom tends to come later in warmer years but that this is not directly correlated with the overall warming trend. The known regime shift of the late 1980s is clearly visible in our data in terms of average phytoplankton winter densities and average cell size, but even so the start of the spring bloom has not changed.

Azaspiracids (AZAs) are a group of lipophilic marine biotoxins associated with human incidents of shellfish poisoning. During a research cruise to the North Sea, we analysed size-fractionated plankton for AZA by mass spectrometry and successfully isolated an AZA-producing dinoflagellate from the east coast of Scotland. As shown previously, an axenic culture of this dinoflagellate produces AZA 1, AZA 2 and an isomer of AZA 2. Here we give a taxonomic description of this new taxon Azadinium spinosum gen. et sp. nov., as a de novo producer of AZAs. Azadinium spinosum is a small (12–16 µm length and 7–11 µm width) peridinin-containing photosynthetic dinoflagellate with a superficial resemblance under light microscopy to gymnodinioids, but with a thin theca. The large nucleus is spherical and located posteriorly, whereas the single chloroplast is parietal, lobed, and typically extends into both the epi- and hyposome. The Kofoidian thecal tabulation is APC, 4′, 3a, 6″, 6C, 5?S, 6′″, 2″″. This plate pattern has an epithecal affinity to the Peridiniales and a hypothecal affinity to the Gonyaulacales, but is distinctly different from described dinoflagellate genera. The assignment of A. spinosum to the dinoflagellates is supported by molecular phylogenetic analysis of four genes, SSU rDNA, LSU rDNA (D1/D2 region), ITS and cytochrome oxidase (sub-unit 1) (COI). In agreement with the morphological description, phylogenetic analysis did not show any particularly close affiliation to the Peridiniales or Gonyaulacales, nor to any other dinoflagellate order represented in molecular databases. Consequently, we erected a new genus, Azadinium, for this taxon. However the ordinal affiliation of the genus is uncertain. This study represents the first description and confirmation of a new dinoflagellate species capable of producing AZA and is thus an important advance in surveillance programmes for toxigenic microalgae and toxins of human health significance.

Our planet is changing, and one of the most pressing challenges facing the scientific community revolves around understanding how ecological communities respond to global changes. From coastal to deep-sea ecosystems, ecologists are exploring new areas of research to find model organisms that help predict the future of life on our planet. Among the different categories of organisms, meiofauna offer several advantages for the study of marine benthic ecosystems. This paper reviews the advances in the study of meiofauna with regard to climate change and anthropogenic impacts. Four taxonomic groups are valuable for predicting global changes: foraminifers (especially calcareous forms), nematodes, copepods and ostracods. Environmental variables are fundamental in the interpretation of meiofaunal patterns and multistressor experiments are more informative than single stressor ones, revealing complex ecological and biological interactions. Global change has a general negative effect on meiofauna, with important consequences on benthic food webs. However, some meiofaunal species can be favoured by the extreme conditions induced by global change, as they can exhibit remarkable physiological adaptations.

Abstract The great variety of geological and hydrological conditions in the deep sea generates many different habitats. Some are only recently explored, although their true extent and geographical coverage are still not fully established. Both continental margins and mid‐oceanic seafloors are much more complex ecologically, geologically, chemically and hydrodynamically than originally thought. As a result, fundamental patterns of species distribution first observed and explained in the context of relatively monotonous slopes and abyssal plains must now be re‐evaluated in the light of this newly recognized habitat heterogeneity. Based on a global database of nematode genus composition, collected as part of the Census of Marine Life, we show that macrohabitat heterogeneity contributes significantly to total deep‐sea nematode diversity on a global scale. Different deep‐sea settings harbour specific nematode assemblages. Some of them, like coral rubble zones or nodule areas, are very diverse habitats. Factors such as increased substrate complexity in the case of nodules and corals seem to facilitate the co‐existence of a large number of genera with different modes of life, ranging from sediment dwelling to epifaunal. Furthermore, strong biochemical gradients in the case of vents or seeps are responsible for the success of particular genera, which are not prominent in more typical soft sediments. Many nematode deep‐sea genera are cosmopolitan, inhabiting a variety of deep‐sea habitats and oceans, whereas only 21% of all deep‐sea genera recorded are restricted to a single habitat. In addition to habitat heterogeneity, regional differences are important in structuring nematode assemblages. For instance, seeps from different regions yield different genera that thrive on the sulphidic sediments. This study also shows that many areas and habitats remain highly under‐sampled, affecting our ability to understand fully the contribution of habitat heterogeneity versus regional differences to global nematode diversity.

ABSTRACT The formation of laminated sand and graded rhythmites — so‐called storm‐sand layers — found embedded in shelf mud is discussed. With decreasing energy of a storm, the sand eroded on the coast is transported away by the retreating waters into the open sea, and is retained in suspension because of the high wave energy of the rough sea. With decreasing wave energy, the individual suspension clouds settle, forming parallel sand layers. As generally only slow bottom currents are present, the sediment deposited is not reformed into ripples, but sedimented in the form of laminated sand.

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 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.

In the recent discussion how biotic systems may react to ocean acidification caused by the rapid rise in carbon dioxide partial pressure (pCO(2)) in the marine realm, substantial research is devoted to calcifiers such as stony corals. The antagonistic process - biologically induced carbonate dissolution via bioerosion - has largely been neglected. Unlike skeletal growth, we expect bioerosion by chemical means to be facilitated in a high-CO(2) world. This study focuses on one of the most detrimental bioeroders, the sponge Cliona orientalis, which attacks and kills live corals on Australia's Great Barrier Reef. Experimental exposure to lowered and elevated levels of pCO(2) confirms a significant enforcement of the sponges' bioerosion capacity with increasing pCO(2) under more acidic conditions. Considering the substantial contribution of sponges to carbonate bioerosion, this finding implies that tropical reef ecosystems are facing the combined effects of weakened coral calcification and accelerated bioerosion, resulting in critical pressure on the dynamic balance between biogenic carbonate build-up and degradation.

The deep sea plays a critical role in global climate regulation through uptake and storage of heat and carbon dioxide. However, this regulating service causes warming, acidification and deoxygenation of deep waters, leading to decreased food availability at the seafloor. These changes and their projections are likely to affect productivity, biodiversity and distributions of deep-sea fauna, thereby compromising key ecosystem services. Understanding how climate change can lead to shifts in deep-sea species distributions is critically important in developing management measures. We used environmental niche modelling along with the best available species occurrence data and environmental parameters to model habitat suitability for key cold-water coral and commercially important deep-sea fish species under present-day (1951-2000) environmental conditions and to project changes under severe, high emissions future (2081-2100) climate projections (RCP8.5 scenario) for the North Atlantic Ocean. Our models projected a decrease of 28%-100% in suitable habitat for cold-water corals and a shift in suitable habitat for deep-sea fishes of 2.0°-9.9° towards higher latitudes. The largest reductions in suitable habitat were projected for the scleractinian coral Lophelia pertusa and the octocoral Paragorgia arborea, with declines of at least 79% and 99% respectively. We projected the expansion of suitable habitat by 2100 only for the fishes Helicolenus dactylopterus and Sebastes mentella (20%-30%), mostly through northern latitudinal range expansion. Our results projected limited climate refugia locations in the North Atlantic by 2100 for scleractinian corals (30%-42% of present-day suitable habitat), even smaller refugia locations for the octocorals Acanella arbuscula and Acanthogorgia armata (6%-14%), and almost no refugia for P. arborea. Our results emphasize the need to understand how anticipated climate change will affect the distribution of deep-sea species including commercially important fishes and foundation species, and highlight the importance of identifying and preserving climate refugia for a range of area-based planning and management tools.

Species distribution models (SDMs) were applied to predict the distribution of benthic species in the North Sea. An understanding of species distribution patterns is essential to gain insight into ecological processes in marine ecosystems and to guide ecosystem management strategies. Therefore, we compared 9 different SDM methods, including GLM, GBM, FDA, SVM, RF, MAXENT, BIOCLIM, GARP and MARS, by using 10 environmental variables to model the distribution of 20 marine benthic species. Most of the models showed good or very good performance in terms of predictive power and accuracy, with highest mean area under the curve (AUC) values of 0.845 and 0.840, obtained for the MAXENT and GBM models, respectively. The poorest performance was shown by the BIOCLIM model, which had a mean AUC of 0.708. Nevertheless, the mapped distribution patterns varied remarkably depending on the model used, with up to 32.5% differences in predictions between models. For species with a narrow distribution range, the models showed a better performance based on the AUC than for species with a broad distribution range, which can most likely be attributed to the restricted spatial scale and the model evaluation procedure. Of the environmental variables, bottom water temperature and depth had the greatest effect on the distribution of 14 benthic species, based on MAXENT results. We examine the potential utility of this strategy for predicting future distribution of benthic species in response to climate change.

Shells of the extremely long-lived bivalve mollusk Arctica islandica (Linnaeus 1767) provide century-long, multi-proxy records of inter-annual environmental variability in middle- to high-latitude marine settings. Reliable interpretation of these climate archives, however, requires exact knowledge of the length and timing of the growing season and which environmental parameters control shell growth rate during the year. Here, intra-annual growth microstructures, δ18O-derived ambient water temperatures, and δ13C from A. islandica shells collected from the southern and central North Sea are studied. Such data were analyzed in conjunction with observational sea-surface temperature and primary productivity data. Arctica islandica produces circadian growth increments in its shell (on average 31.5 μm per day during age four, measured along the outer shell surface), which allow assignment of calendar dates to each shell portion. The growing season of A. islandica in the upper mixed layer of the ocean (here 25 m water depth) is not continuous over an eight-month period as previously suggested. Rather, it is interrupted during spawning between early September and mid-November. In addition, shell production ceases or is strongly retarded due to food scarcity between mid-December and mid-February. Water temperatures derived from oxygen-isotope ratios are in good accord with observed sea-surface temperatures. In specimens at 25 m water depth, abrupt changes in shell δ18O-derived temperature (Tδ18O) were interpreted to represent vertical displacements of the seasonal thermocline. Daily shell growth is controlled by temperature and food availability. Up to 58% of the variation in daily growth rate is explained by these environmental parameters. This study demonstrates that A. islandica can provide seasonal to subseasonal, precisely dated proxies of environmental variables. Such data are of increasing importance for climate models.

Bioerosion of calcium carbonate is the natural counterpart of biogenic calcification. Both are affected by ocean acidification (OA). We summarize definitions and concepts in bioerosion research and knowledge in the context of OA, providing case examples and meta-analyses. Chemically mediated bioerosion relies on energy demanding, biologically controlled undersaturation or acid regulation and increases with simulated OA, as does passive dissolution. Through substrate weakening both processes can indirectly enhance mechanical bioerosion, which is not directly affected by OA. The low attention and expert knowledge on bioerosion produced some ambiguous views and approaches, and limitations to experimental studies restricted opportunities to generalize. Comparability of various bioerosion and calcification rates remains difficult. Physiological responses of bioeroders or interactions of environmental factors are insufficiently studied. We stress the importance to foster and advance high quality bioerosion research as global trends suggest the following: (i) growing environmental change (eutrophication, coral mortality, OA) is expected to elevate bioerosion in the near future; (ii) changes harmful to calcifiers may not be as severe for bioeroders (e.g. warming); and (iii) factors facilitating bioerosion often reduce calcification rates (e.g. OA). The combined result means that the natural process bioerosion has itself become a “stress factor”” for reef health and resilience.