Description: Microplastics in aquatic ecosystems and especially in the marine environment represent a pollution of increasing scientific and societal concern, thus, meanwhile a substantial number of studies on microplastics exist. Although first steps towards a standardisation of methodologies used for the detection and identification of microplastics in environmental samples are made, the comparability of data on microplastics is currently hampered by a huge variety of different methodologies which result in the generation of data of extremely different quality and resolution. This chapter reviews the methodology presently used for assessing the concentration of microplastics in the marine environment with focus on the most convenient techniques and approaches. After an overview of non-selective sampling approaches, sample processing and treatment in the laboratory, the reader is introduced to the currently applied techniques for the identification and quantification of microplastics. The subsequent case study on microplastics in sediment samples from the North Sea measured with focal plane array (FPA)-based micro-Fourier transform infrared (micro-FTIR) spectroscopy shows that only 1.4 % of the particles visually resembling microplastics were of synthetic polymer origin. This finding emphasizes the importance of verifying the synthetic polymer origin of potential microplastics. Thus, a burning issue concerning current microplastic research is the generation of standards that allow for the assessment of reliable data on concentrations of microscopic plastic particles and the involved polymers with analytical laboratory techniques such as micro-FTIR or micro-Raman spectroscopy.

Description: Microbiota provide their hosts with a range of beneficial services, including defense from external pathogens. However, host-associated microbial communities themselves can act as a source of opportunistic pathogens depending on the environment. Marine poikilotherms and their microbiota are strongly influenced by temperature, but experimental studies exploring how temperature affects the interactions between both parties are rare. To assess the effects of temperature, temperature stress and infection on diversity, composition and dynamics of the hemolymph microbiota of Pacific oysters (Crassostrea gigas), we conducted an experiment in a fully-crossed, three-factorial design, in which the temperature acclimated oysters (8 or 22 °C) were exposed to temperature stress and to experimental challenge with a virulent Vibrio sp. Strain. We monitored oyster survival and repeatedly collected hemolymph of dead and alive animals to determine the microbiome composition by 16s rRNA gene amplicon pyrosequencing. We found that the microbial dynamics and composition of communities in healthy animals (including infection survivors) were significantly affected by temperature and temperature stress, but not by infection. The response was mediated by changes in the incidence and abundance of operational taxonomic units (OTUs) and accompanied by little change at higher taxonomic levels, indicating dynamic stability of the hemolymph microbiome. Dead and moribund oysters, on the contrary, displayed signs of community structure disruption, characterized by very low diversity and proliferation of few OTUs. We can therefore link short-term responses of host-associated microbial communities to abiotic and biotic factors and assess the potential feedback between microbiota dynamics and host survival during disease.

Description: Floating anthropogenic litter provides habitat for a diverse community of marine organisms. A total of 387 taxa, including pro- and eukaryotic micro-organisms, seaweeds and invertebrates, have been found rafting on floating litter in all major oceanic regions. Among the invertebrates, species of bryozoans, crustaceans, molluscs and cnidarians are most frequently reported as rafters on marine litter. Microorganisms are also ubiquitous on marine litter although the composition of the microbial community seems to depend on specific substratum characteristics such as the polymer type of floating plastic items. Sessile suspension feeders are particularly well-adapted to the limited autochthonous food resources on artificial floating substrata and an extended planktonic larval development seems to facilitate colonization of floating litter at sea. Properties of floating litter, such as size and surface rugosity, are crucial for colonization by marine organisms and the subsequent succession of the rafting community. The rafters themselves affect substratum characteristics such as floating stability, buoyancy, and degradation. Under the influence of currents and winds marine litter can transport associated organisms over extensive distances. Because of the great persistence (especially of plastics) and the vast quantities of litter in the world’s oceans, rafting dispersal has become more prevalent in the marine environment, potentially facilitating the spread of invasive species.

Description: Global warming was reported to cause growth reductions in tropical shallow water corals in both, cooler and warmer, regions of the coral species range. This suggests regional adaptation with less heat-tolerant populations in cooler and more thermo-tolerant populations in warmer regions. Here, we investigated seasonal changes in the in situ metabolic performance of the widely distributed hermatypic coral Pocillopora verrucosa along 12 degrees latitudes featuring a steep temperature gradient between the northern (28.5 degrees N, 21-27 degrees C) and southern (16.5 degrees N, 28-33 degrees C) reaches of the Red Sea. Surprisingly, we found little indication for regional adaptation, but strong indications for high phenotypic plasticity: Calcification rates in two seasons (winter, summer) were found to be highest at 28-29 degrees C throughout all populations independent of their geographic location. Mucus release increased with temperature and nutrient supply, both being highest in the south. Genetic characterization of the coral host revealed low inter-regional variation and differences in the Symbiodinium clade composition only at the most northern and most southern region. This suggests variable acclimatization potential to ocean warming of coral populations across the Red Sea: high acclimatization potential in northern populations, but limited ability to cope with ocean warming in southern populations already existing at the upper thermal margin for corals

Description: This book describes how manmade litter, primarily plastic, has spread into the remotest parts of the oceans and covers all aspects of this pollution problem from the impacts on wildlife and human health to socio-economic and political issues. Marine litter is a prime threat to marine wildlife, habitats and food webs worldwide. The book illustrates how advanced technologies from deep-sea research, microbiology and mathematic modelling as well as classic beach litter counts by volunteers contributed to the broad awareness of marine litter as a problem of global significance. The authors summarise more than five decades of marine litter research, which receives growing attention after the recent discovery of great oceanic garbage patches and the ubiquity of microscopic plastic particles in marine organisms and habitats. In 16 chapters, authors from all over the world have created a universal view on the diverse field of marine litter pollution, the biological impacts, dedicated research activities, and the various national and international legislative efforts to combat this environmental problem. They recommend future research directions necessary for a comprehensive understanding of this environmental issue and the development of efficient management strategies. This book addresses scientists, and it provides a solid knowledge base for policy makers, NGOs, and the broader public.

Description: The symbiotic association of corals and unicellular algae of the genus Symbiodinium in the southern Persian/Arabian Gulf (PAG) display an exceptional heat tolerance, enduring summer peak temperatures of up to 36 °C. As yet, it is not clear whether this resilience is related to the presence of specific symbiont types that are exclusively found in this region. Therefore, we used molecular markers to identify the symbiotic algae of three Porites species along 〉1000 km of coastline in the PAG and the Gulf of Oman and found that a recently described species, Symbiodinium thermophilum, is integral to coral survival in the southern PAG, the world’s hottest sea. Despite the geographic isolation of the PAG, we discovered that representatives of the S. thermophilum group can also be found in the adjacent Gulf of Oman providing a potential source of thermotolerant symbionts that might facilitate the adaptation of Indian Ocean populations to the higher water temperatures expected for the future. However, corals from the PAG associated with S. thermophilum show strong local adaptation not only to high temperatures but also to the exceptionally high salinity of their habitat. We show that their superior heat tolerance can be lost when these corals are exposed to reduced salinity levels common for oceanic environments elsewhere. Consequently, the salinity prevailing in most reefs outside the PAG might represent a distribution barrier for extreme temperature-tolerant coral/Symbiodinium associations from the PAG.

Description: This manual represents a review of the potential sources and methods to be applied when providing prior information to Bayesian stock assessments and marine risk analysis. The manual is compiled as a product of the EC Framework 7 ECOKNOWS project (www.ecoknows.eu). The manual begins by introducing the basic concepts of Bayesian inference and the role of prior information in the inference. Bayesian analysis is a mathematical formalization of a sequential learning process in a probabilistic rationale. Prior information (also called ”prior knowledge”, ”prior belief”, or simply a ”prior”) refers to any existing relevant knowledge available before the analysis of the newest observations (data) and the information included in them. Prior information is input to a Bayesian statistical analysis in the form of a probability distribution (a prior distribution) that summarizes beliefs about the parameter concerned in terms of relative support for different values. Apart from specifying probable parameter values, prior information also defines how the data are related to the phenomenon being studied, i.e. the model structure. Prior information should reflect the different degrees of knowledge about different parameters and the interrelationships among them. Different sources of prior information are described as well as the particularities important for their successful utilization. The sources of prior information are classified into four main categories: (i) primary data, (ii) literature, (iii) online databases, and (iv) experts. This categorization is somewhat synthetic, but is useful for structuring the process of deriving a prior and for acknowledging different aspects of it. A hierarchy is proposed in which sources of prior information are ranked according to their proximity to the primary observations, so that use of raw data is preferred where possible. This hierarchy is reflected in the types of methods that might be suitable – for example, hierarchical analysis and meta-analysis approaches are powerful, but typically require larger numbers of observations than other methods. In establishing an informative prior distribution for a variable or parameter from ancillary raw data, several steps should be followed. These include the choice of the frequency distribution of observations which also determines the shape of prior distribution, the choice of the way in which a dataset is used to construct a prior, and the consideration related to whether one or several datasets are used. Explicitly modelling correlations between parameters in a hierarchical model can allow more effective use of the available information or more knowledge with the same data. Checking the literature is advised as the next approach. Stock assessment would gain much from the inclusion of prior information derived from the literature and from literature compilers such as FishBase (www.fishbase.org), especially in data-limited situations. The reader is guided through the process of obtaining priors for length–weight, growth, and mortality parameters from FishBase. Expert opinion lends itself to data-limited situations and can be used even in cases where observations are not available. Several expert elicitation tools are introduced for guiding experts through the process of expressing their beliefs and for extracting numerical priors about variables of interest, such as stock–recruitment dynamics, natural mortality, maturation, and the selectivity of fishing gears. Elicitation of parameter values is not the only task where experts play an important role; they also can describe the process to be modelled as a whole. Information sources and methods are not mutually exclusive, so some combination may be used in deriving a prior distribution. Whichever source(s) and method(s) are chosen, it is important to remember that the same data should not be used twice. If the 2 | ICES Cooperative Research Report No. 328 plan is to use the data in the analysis for which the prior distribution is needed, then the same data cannot be used in formulating the prior. The techniques studied and proposed in this manual can be further elaborated and fine-tuned. New developments in technology can potentially be explored to find novel ways of forming prior distributions from different sources of information. Future research efforts should also be targeted at the philosophy and practices of model building based on existing prior information. Stock assessments that explicitly account for model uncertainty are still rare, and improving the methodology in this direction is an important avenue for future research. More research is also needed to make Bayesian analysis of non-parametric models more accessible in practice. Since Bayesian stock assessment models (like all other assessment models) are made from existing knowledge held by human beings, prior distributions for parameters and model structures may play a key role in the processes of collectively building and reviewing those models with stakeholders. Research on the theory and practice of these processes will be needed in the future.