Micro-computed tomography (micro-CT or microtomography) is a non-destructive imaging technique using X-rays which allows the digitisation of an object in three dimensions. The ability of micro-CT imaging to visualise both internal and external features of an object, without destroying the specimen, makes the technique ideal for the digitisation of valuable natural history collections. This handbook serves as a comprehensive guide to laboratory micro-CT imaging of different types of natural history specimens, including zoological, botanical, palaeontological and geological samples. The basic principles of the micro-CT technology are presented, as well as protocols, tips and tricks and use cases for each type of natural history specimen. Finally, data management protocols and a comprehensive list of institutions with micro-CT facilities, micro-CT manufacturers and relative software are included.

The study of ecosystem functioning – the role which organisms play in an ecosystem – is becoming increasingly important in marine ecological research. The functional structure of a community can be represented by a set of functional traits assigned to behavioural, reproductive and morphological characteristics. The collection of these traits from the literature is however a laborious and time-consuming process, and gaps of knowledge and restricted availability of literature are a common problem. Trait data are not yet readily being shared by research communities, and even if they are, a lack of trait data repositories and standards for data formats leads to the publication of trait information in forms which cannot be processed by computers. This paper describes Polytraits (http://polytraits.lifewatchgreece.eu), a database on biological traits of marine polychaetes (bristle worms, Polychaeta: Annelida). At present, the database contains almost 20,000 records on morphological, behavioural and reproductive characteristics of more than 1,000 marine polychaete species, all referenced by literature sources. All data can be freely accessed through the project website in different ways and formats, both human-readable and machine-readable, and have been submitted to the Encyclopedia of Life for archival and integration with trait information from other sources.

Marine hard-bottom communities are undergoing severe change under the influence of multiple drivers, notably climate change, extraction of natural resources, pollution and eutrophication, habitat degradation, and invasive species. Monitoring marine biodiversity in such habitats is, however, challenging as it typically involves expensive, non-standardized, and often destructive sampling methods that limit its scalability. Differences in monitoring approaches furthermore hinders inter-comparison among monitoring programs. Here, we announce a Marine Biodiversity Observation Network (MBON) consisting of Autonomous Reef Monitoring Structures (ARMS) with the aim to assess the status and changes in benthic fauna with genomic-based methods, notably DNA metabarcoding, in combination with image-based identifications. This article presents the results of a 30-month pilot phase in which we established an operational and geographically expansive ARMS-MBON. The network currently consists of 20 observatories distributed across European coastal waters and the polar regions, in which 134 ARMS have been deployed to date. Sampling takes place annually, either as short-term deployments during the summer or as long-term deployments starting in spring. The pilot phase was used to establish a common set of standards for field sampling, genetic analysis, data management, and legal compliance, which are presented here. We also tested the potential of ARMS for combining genetic and image-based identification methods in comparative studies of benthic diversity, as well as for detecting non-indigenous species. Results show that ARMS are suitable for monitoring hard-bottom environments as they provide genetic data that can be continuously enriched, re-analyzed, and integrated with conventional data to document benthic community composition and detect non-indigenous species. Finally, we provide guidelines to expand the network and present a sustainability plan as part of the European Marine Biological Resource Centre (www.embrc.eu).

The anabolic effect of exercise on muscles and bones is well documented. In teleost fish, exercise has been shown to accelerate skeletogenesis, to increase bone volume, and to change the shape of vertebral bodies. Still, increased swimming has also been reported to induce malformations of the teleost vertebral column, particularly lordosis. This study examines whether zebrafish (Danio rerio) develops lordosis as a result of continuous physical exercise. Zebrafish were subjected, for 1 week, to an increased swimming exercise of 5.0, 6.5 or 8.0 total body lengths (TL) per second. Control and exercise group zebrafish were examined for the presence of vertebral abnormalities, by in vivo examination, whole mount staining for bone and cartilage and histology and micro‐computed tomography (CT) scanning. Exercise zebrafish developed a significantly higher rate of lordosis in the haemal part of the vertebral column. At the end of the experiment, the frequency of lordosis in the control groups was 0.5 ± 1.3% and that in the exercise groups was 7.5 ± 10.6%, 47.5 ± 10.6% and 92.5 ± 6.0% of 5.0, 6.5 and 8.0 TL∙s−1, respectively. Histological analysis and CT scanning revealed abnormal vertebrae with dorsal folding of the vertebral body end plates. Possible mechanisms that trigger lordotic spine malformations are discussed. This is the first study to report a quick, reliable and welfare‐compatible method of inducing skeletal abnormalities in a vertebrate model during the post‐embryonic period.

The increased absorption of atmospheric CO2 by the ocean affects carbonate chemistry and calcification rates of marine organisms. The impacts of low pH and seawater warming were investigated for the intertidal gastropods Nassarius nitidus and Columbella rustica. The combined effect of reduced pH (7.6) and increased temperature (25 °C) was studied at intermediate time intervals for a total period of 3 months in order to investigate variability and fluctuations of the shell structure and density over time. The pH and temperature conditions used for the experiment were selected according to the predictions of the Intergovernmental Panel on Climate Change. Deterioration of the external surface structure and reduction of shell density of the gastropods were confirmed using an innovative imaging and analysis method based on micro-computed tomography. The effect of low pH at ambient temperature was detrimental for N. nitidus with a 38.1% reduction of density in the shell lip and a 47.7% decrease in the apex, which is the oldest shell region. C. rustica was also affected, although to a much lesser degree (the maximum reduction observed was 8% at the apex). The negative effects of reduced pH were further reinforced for C. rustica when the temperature was increased, while N. nitidus was not affected significantly by the combination of the two factors. Increased temperature at ambient pH had an inhibitory effect on the shell density of N. nitidus causing a reduction of about 40%, whereas the shell density of the widest and lip regions of the C. rustica were increased under the same conditions. Different species are characterised by different vulnerability and tolerance responses regarding ocean acidification and warming, and this variability may affect ecological interactions and marine biodiversity.

Mud volcanoes are a~special type of cold seeps where life is based on chemoautotrophic processes. They are considered to be extreme environments and are characterized by unique megafaunal and macrofaunal communities. However, very few studies on mud volcanoes taking into account the smaller meiobenthic communities have been carried out. Two mud volcanoes were explored during the MEDECO (MEditerranean Deep-sea ECOsystems) cruise (2007) with the remotely operated vehicle (ROV) Victor-6000: Amsterdam, located south of Turkey between 1700 and 2000 m depth (Anaximander mud field); and Napoli, south of Crete, located along the Mediterranean Ridge at about 2000 m depth (Olimpi mud field). The major aim of this study was to describe distributional patterns of meiofaunal communities and nematode assemblages from different seep microhabitats. Meiofaunal taxa and nematode assemblages at both mud volcanoes differed significantly from other Mediterranean sites in terms of standing stocks, dominance and species diversity. Density and biomass values were significantly higher at the seep sites, particularly at Amsterdam. Patterns of nematode diversity, the dominant meiofaunal taxon, varied, displaying both very high or very low species richness and dominance, depending on the microhabitat studied. The periphery of the Lamellibrachia and bivalve shell microhabitats of Napoli exhibited the highest species richness, while the reduced sediments of Amsterdam yielded a species-poor nematode community dominated by two successful species, one belonging to the genus Aponema and the other to the genus Sabatieria. Analysis of β-diversity showed that microhabitat heterogeneity of mud volcanoes contributed substantially to the total nematode species richness in the eastern Mediterranean Sea. These observations indicate a strong influence of mud volcanoes and cold-seep ecosystems on the meiofaunal communities and nematode assemblages

Long-term exposure to elevated pCO 2 more than warming modifies early-life shell growth in a temperate gastropod. -ICES Journal of Marine Science, doi:10.1093/icesjms/fsw242. Co-occurring global change drivers, such as ocean warming and acidification, can have large impacts on the behaviour, physiology, and health of marine organisms. However, whilst early-life stages are thought to be most sensitive to these impacts, little is known about the individual level processes by which such impacts take place. Here, using mesocosm experiments simulating ocean warming (OW) and ocean acidification (OA) conditions expected for the NE Atlantic region by 2100 using a variety of treatments of elevated pCO 2 and temperature. We investigated their impacts on bio-mineralization, microstructure, and ontogeny of Nucella lapillus (L.) juveniles, a common gastropod predator that exerts important top-down controls on biodiversity patterns in temperate rocky shores. The shell of juveniles hatched in mesocosms during a 14 month long experiment were analysed using micro-CT scanning, 3D geometric morphometrics, and scanning-electron microscopy. Elevated temperature and age determined shell density, length, width, thickness, elemental chemistry, shape, and shell surface damages. However, co-occurring elevated pCO 2 modified the impacts of elevated temperature, in line with expected changes in carbonate chemistry driven by temperature. Young N. lapillus from acidified treatments had weaker shells and were therefore expected to be more vulnerable to predation and environmental pressures such as wave action. However, in some instances, the effects of both higher CO 2 content and elevated temperature appeared to have reversed as the individuals aged. This study suggests that compensatory development may therefore occur, and that expected increases in juvenile mortality under OA and OW may be counteracted, to some degree, by high plasticity in shell formation in this species. This feature may prove advantageous for N. lapillus community dynamics in near-future conditions.

This paper describes a dataset of polychaetes (Annelida) from 14 midlittoral rocky shore sampling sites in Greece and Italy (Mediterranean Sea). The dataset combines the outcome of four different projects studying the hard substrate midlittoral zone in the Mediterranean between 1984 and 2009. Samples were collected by scraping and collecting the organisms from a framed area. The maximal sampling depth was 1.5 m. In total, 123 polychaete species were recorded, five of which are new records for the respective biogeographic sectors of the Mediterranean. The dataset contains 788 occurrence records, fully annotated with all required metadata. These data contribute to the knowledge of a previously very understudied regional habitat, since at present, comprehensive lists of the midlittoral communities in the Mediterranean are provided through only a few, paper-based, studies. This dataset is one of the first electronic data compilations of the Mediterranean midlittoral zone communities and certainly the most comprehensive of its kind, contributing to the ongoing efforts of the Ocean Biogeographic Information System (OBIS) which aims at filling the gaps in our current knowledge of the world's oceans. It is accessible at http://ipt.vliz.be/resource.do?r=mediterraneanpolychaetaintertidal.