Sampling cruises were carried out on three coastal stations of the northern Ionian Sea over one year to investigate the effects of environmental factors on phytoplankton and picophytoplankton composition and succession. Larger phytoplankton (micro and nano fractions) was determined by using the Utermöhl settling technique, while picophytoplankton fraction was determined by epifluorescence microscopy. Furthermore, microbiological procedures were applied to investigate cyanobacterial diversity in the studied area. Results suggested that the most striking feature of phytoplankton communities was the high spatial variability in terms of abundance and biomass, which showed specific coastal Mediterranean values. Undetermined phytoflagellates and diatoms were the dominant groups of the Utermöhl fraction of phytoplankton, while round to rod-shaped small sized cyanobacteria represented the picophytoplankton fraction. Our data suggested that in the northern Ionian Sea the phytoplankton development was related to phosphorus availability and to ‘nitrogen-rich’ waters. Also the picophytoplankton seasonal trend was significantly correlated to N-compounds as well as to water temperature.

In addition to the typical picoplanktonic Synechococcus, the culture techniques allowed us to isolate and identify cyanobacteria belonging to the pleurocapsalean genus Stanieria and the oscillatoriacean genera Geitlerinema, Leiblenia, Leptolyngbya, Oscillatoria, Pseudanabaena and Spirulina. These species represent a minor fraction of the total cyanobacterial community in terms of biomass, but their importance is related to their contribution to the phytoplankton diversity.

Macrofaunal assemblages inhabiting stable offshore muddy sand substrata responded predictably to the effects of mild organic enrichment arising from sewage-sludge disposal off the north-east coast of England (western North Sea). At the disposal site, densities were elevated up to two-fold, but classical ‘indicator’ species were only marginally enhanced and there was no evidence of a significant waste-induced change in assemblage structure. The response following cessation of disposal was equally predictable, with a decline in densities to ‘reference’ levels some three years later. However, physical manifestations of disposal, including tomato pips and non-biodegradable artefacts, were still evident after this time.

Changes in diversity at selected monitoring stations tended to track each other over time and the employment of treatment/reference ratios and limit values for acceptable change provided a useful model for the simplified expression of trends. Predictions concerning the limited scale and intensity of the effects of sewage-sludge disposal appear to have been met, indicating that the management option of sea disposal was, at the time, an environmentally acceptable one.

Temporal trends in the benthic fauna were also correlated with winter values of the North Atlantic Oscillation Index for the preceding year. The densities and variety of species tended to be lower in response to warmer winters characterized by westerly airflows which were commonly encountered in the 1990s. Finally, the increasing importance of extended time-series data for the investigation of man-made impacts on the marine environment is highlighted, along with the accompanying requirement for continuity and quality assurance of sampling programmes.

The relationships between phytoplankton pigments, optical properties and photosynthetic parameters for different phytoplankton functional types (derived by diagnostic pigment indices, DPI) were determined from data acquired in the Benguela ecosystem and the offshore region in October 2002. We observed robust inter-pigment relationships: total chlorophyll-a (TChla) was highly correlated with total pigment (TP) and accessory pigment (AP). However, the regression equations for stations dominated by flagellates differed from the equations for stations dominated by diatoms and dinoflagellates. The pigment ratio TChla/TP and the optical ratio a676/a440 were not constant but increased non-linearly with increasing TChla or TP; complimentarily the AP/TP and a490/a676 ratios decreased. There were significant non linear relationships between the photosynthetic parameters Fv/Fm or σPSII measured by Fast Repetition Rate Fluorometry and TChla or TP. Pigment ratios, optical ratios, Fv/Fm and σPSII were all inter-correlated with high significance. We determined the distinctive bio-optical properties associated with dominant phytoplankton functional types (derived by DPI) that conformed to the classical partitioning: flagellates (nano-plankton, comprising several taxa) had low biomass,low TChla/TP fraction and low Fv/Fm and high σPSII; diatoms and dinoflagellates (micro-plankton) had high biomass, pigment ratios, Fv/Fm and low σPSII.

Rotifers are microscopic aquatic animals that comprise more than 1800 species. Most rotifer species live in freshwater and limno-terrestrial habitats, while thalassic environments (brackish+seawater) are thought to host few species. No recent review of saline rotifers is available. Here we report the results of a review of the literature concerning rotifers from saline environments, distinguished into three categories: stenohaline, euryhaline, and haloxenous, and found both in truly marine habitats and/or in inland saline waters. A total of about 200 studies, mentioning fully identified rotifers from saline waters, allowed us to list as many as 443 rotifer taxa at either specific, subspecific and infrasubspecific rank, corresponding to 391 nominal species. Truly thalassic taxa, not found in inland saline waters only, accounted for 289, including the ‘stenohaline’ (143) and the euryhaline (146) ones. As for freshwaters, the majority of the thalassic rotifers inhabit the psammon, or display a benthic–periphytic way of life, while the plankton likewise is less species rich and less abundant. The geographical distribution of the brackish and marine rotifers largely reflects the distribution of rotifer investigators, therefore, no biogeographical analysis can be performed yet. In conclusion, the analysis of literature citing rotifers in salt waters, uncovers an unexpected rotifer fauna: the apparent richness of the group in thalassic environments is worthy of being addressed by further investigations, as many species have been reported only by their description, suggesting either considerable endemism or taxonomic errors.

The higher taxonomic structure of the meiofaunal community was investigated in three eastern Mediterranean lagoons, an open (Vassova), a semi-closed (Piges) and a closed lagoon (Alykes Kitrous). In total, 22 stations representing characteristic features in each lagoon were sampled. Stations were found to support a maximum of 19 meiofaunal taxa with densities ranging from 1 to 10,000 individuals per 10 cm2. Nematodes were dominant at all sites (30–97%) except at the hypersaline sites, where ciliates outnumbered all metazoan meiofaunal taxa (53–77%). Uni- and multivariate analyses were applied to study the community structure. The number of taxa and the meiofaunal density showed strong spatial differences in all three lagoons; however, the main source of variation occurred between the semi-closed and closed lagoons. Both the meiofaunal composition and density were significantly less at the hypersaline sites which had salinity above 100 psu. The meiofaunal distribution pattern was shown to be controlled by abiotic factors, in particular vertical stratification of salinity, bottom water currents and oxygen availability at the bottom water–sediment interface. However, the distribution of feeding resources (e.g. cyanobacteria, phytodetritus) was also found to play a key role in structuring meiofaunal communities.

It is likely that all living organisms can be infected by one or more viruses. One of the latest higher taxa to be converted from ‘no characterized viruses’ to ‘well characterized viruses’ are the diatoms (Bacillariophyceae, Heterokontophyta) with the recent publication of three papers characterizing an ssRNA and a ssDNA virus from two genera (Chaetoceros and Rhizosolenia) of marine planktonic diatom (Nagasaki et al., 2004, 2005; Bettarel et al., 2005). It would have been strange if viruses had not been able to exploit the dominant, in terms of global primary production, photosynthetic organisms in the ocean (assimilating perhaps as much as 20 Pg inorganic C into organic C per year), despite the less than completely convincing arguments assembled by Raven & Waite (2004) as to possible anti-viral defences unique to diatoms.

The New Zealand cockle Austrovenus stutchburyi is often found stranded on the sediment surface due to infections by echinostome trematodes. High densities of heavily-infected cockles on the sediment surface affect near-seabed hydrodynamics and sedimentation and, in turn, benthic animal community structure and diversity. In a six-month field experiment on an intertidal sandflat we manipulated the density of cockle mimics on the sediment surface, and here we show that their presence had two significant impacts on community functioning. First, the benthic primary production (in terms of chlorophyll-a content) was reduced by 8–22%. Second, their presence significantly boosted (up to 5-fold) the secondary production (in terms of biomass) of Coelenterata, Nemertea, small polychaetes, small bivalves and the gastropod Diloma subrostrata. The results hence provide a field experimental example of a parasite-mediated link between diversity and productivity.

Mesozooplankton was sampled during one year in the eutrophicated Vranjic Basin and the influence of environmental variables on its abundance and distribution was analysed. Parallel microzooplankton samples were collected in order to assess trophic relationships within the zooplankton community. Total mesozooplankton abundances were high, exceeding 2×104 ind m−3 in the warmer part of the year, but the biodiversity was low. The annual variability of this assemblage was mostly influenced by temperature. Copepods were dominant among net plankton groups, while ciliates dominated the protozoan community. The key species of the copepod community were Acartia clausi, Oithona nana and Euterpina acutifrons, occurring simultaneously throughout the year. High abundances of small copepod Oithona nana were determined in both meso- and microzooplankton samples, and comparisons of the catches from 125 μm net and 5-l Niskin bottles revealed no significant differences between them. Significant correlation determined between Acartia clausi and oligotrich ciliates indicates predator–prey relationship and the importance of the ciliate community in the energy transfer through the trophic web of this area.

Two new species of rotifer belonging to the Dicranophoridae, and provisionally placed in the genus Encentrum, are described from littoral psammon from the Ussuriyskiy Bay, Peter the Great Bay, Sea of Japan, Russia. Encentrumkutikovae sp. nov. is characterized by a long foot consisting of three pseudosegments, cylindrical toes, a hexagonal rami outline, and the right ramus showing an accessory chamber with alula. Encentrum ussuriensis sp. nov. is characterized by unusual stout toes with claw, an oblong-ovate and latero-caudal weakly angular rami outline, the right ramus bearing an alula, and the left one showing an accessory chamber.

Viruses are the most abundant members of marine ecosystems and play an enormous role in ocean processes through their interactions with all types of marine organisms. This short review provides examples of the dramatic increase in our knowledge of the diversity of marine viruses as pathogens of bacteria, protists, molluscs, crustaceans, cnidaria, reptiles, fish and mammals. Several examples are provided showing evidence of evolution of new strains, changes in virulence, and transfer of viruses between ecosystems. The natural and anthropogenic causes of these shifts are discussed. Despite considerable advances in recent years, knowledge of the importance of viruses in many important groups of marine organisms is lacking or incomplete. Suggestions for future investigations necessary to understand the dynamics of biogeochemical processes and the impacts of disease in our oceans are proposed.

The molecular diversity of dinoflagellate algae of the genus Symbiodinium in symbiosis with ten species of scleractinian coral, sea anemone and scyphomedusa in the Mediterreanean Sea was investigated by restriction analysis and sequencing of polymerase chain reaction-amplified fragments of SSU and LSU rRNA genes. All species bore Symbiodinium of clade A, apart from Bunodeopsis strumosa, which had clade B. The clade A sequences clustered with a previously described group, ‘temperate-A’, known only from the Mediterranean and Atlantic coasts of the UK and France. It is concluded that clade temperate-A is prevalent, but not universal, in the Mediterranean.

Video transects of epibenthic communities provide a valuable and non-destructive surveying methodology. The use of unstable platforms for video collection, such as divers and remotely operated vehicles, can lead to variation in the field of view, and consequently the dimensions of the surveyed area. Unless this can be accounted for, quantifying the species present can be time consuming or unworkable. Use of time-based, rather than areas-based, enumeration techniques, such as the visual fast count (VFC), can overcome this variation. Using seabed video footage from Strangford Lough, the reliability of the VFC was assessed through comparison with direct counts. Multivariate analysis of variance indicates that data derived from the VFC did not differ from that obtained from direct counts. Pairwise comparisons between locations in Strangford Lough using analysis of similarities (PRIMER) also indicated good agreement between the two methods. Use of the VFC method therefore provides: (1) a reliable alternative to direct counts for epibenthic enumeration; (2) a substantial reduction in post-survey processing time and; (3) a method capable of allowing variation in the visual field/sampled area.

Within a subtropical estuary in southern Brazil, an experiment was carried out to test the hypotheses that the deposit feeding macrofaunal polychaete Laeonereis acuta affects nematode community structure and the vertical distribution patterns of nematodes in sediments. Inclusion cages were deployed with two different densities of the polychaete and meiofaunal nematodes were sampled from six different vertical sediment layers: 0–1, 1–2, 2–4, 4–6, 6–8 and 8–10 cm depth. Although L. acuta did change the vertical distribution of both nematode and trophic groups in the sediment, allowing nematodes to inhabit deeper sediment layers, there were no apparent effects of different polychaete densities.

Lough Hyne time series records showed a clear increase in vertical mixing associated with spring tides. Temperature records from the thermocline region were the most variable of the depths studied with differences of up to 0.7°C between readings taken 3 min apart.

‘Reefs’ are listed under Annex I of the Habitats Directive as a marine habitat to be protected by the designation of Special Areas of Conservation. Crucially for the implementation of the Directive, the distinction between what is considered as ‘reef’ and what is not is imprecise, particularly in relation to colonies of the tube-building polychaete Sabellaria spinulosa. Guidelines are proposed for the implementation of the Habitats Directive definition to provide a robust and transparent approach for the benefit of both regulators and offshore industry. Specifically, it is suggested that the conservation priority of a S. spinulosa aggregation could be determined using a scoring system based on a series of physical, biological and temporal characteristic reef features, weighted according to the perceived importance of each feature and augmented with a further score indicating the confidence in the feature score. Suggestions are given as to how these characteristics might be measured and scored, along with an example to illustrate the application of the approach.

Phytopigment concentrations (chlorophyll-a and phaeopigments), labile organic matter (proteins, carbohydrates and lipids), bacterial density and frequency of dividing cells were analysed in the sediments of a large coastal area covering the southern Adriatic continental shelf between Italy and Albania in order to describe the trophic status of coastal marine sediments. On average, sediments of the Italian coast displayed the highest phytopigment and biopolymeric carbon concentrations compared to sediments of the Albanian coast and indicated an increased nutritional status of this coastal ecosystem. Different trophic conditions were evidenced in terms of biopolymeric composition of sedimentary organic matter as an increase in protein and a decrease in the carbohydrate contributions to total biopolymeric carbon was observed moving from the Albanian to the Italian coast. Using a benthic approach for the evaluation of trophic status shallow Italian sediments (0–50 m) were mainly classified as eutrophic and were subjected to stronger anthropogenic disturbance. This was particularly evident in areas in front of city harbours (Brindisi and Barletta) that were classified as hypertrophic and displayed the highest biopolymeric carbon (BPC) concentrations and protein to carbohydrate ratio (PRT:CHO on average >1). In contrast Albanian sediments as well as deeper Italian stations (>50 m), resulted mainly in meso-oligotrophic and displayed lower BPC and PRT:CHO ratio (on average <1). The study of bacterial variables provided an improved approach for the conceptual definition of trophic state using benthic biochemical measures. An inverse relationship occurred between the nutritional contents and the bacterial density within meso-oligotrophic sediments. This may reflect an increase in ecosystem organization and complexity (i.e. increased abundance of the higher trophic levels) which may determine a reduction of the bacterial density at increasing trophic conditions. In contrast a positive correlation was found within eutrophic and hypertrophic sediments suggesting that at high organic matter concentrations the ecosystem is no longer capable of further organization.

The relationships between three species of thecate hydrozoans, Sertularella crassicaulis, Sertularella ellisii and Aglaophenia tubiformis with three species of encrusting Corallinales, Pneophyllum fragile, Melobesia membranacea and Hydrolithon cf. farinosum from different locations in the western Mediterranean are described. In Aglaophenia tubiformis, algae were observed on the hydrotheca, while in Sertularella spp. they grew on the stem, the branches and the hydrothecae which became completely covered by encrusting, calcified thalli. The polyps were living in the covered theca. The hydroid species hosting Corallinales were a small fraction of the entire assemblages and this evidence suggests that hydroids cannot be considered as a simple, inert substrate. We hypothesize that this specificity could be explained by a different molecular composition of hydroid exoskeletons, and/or production of secondary metabolites that affect organism settlement. Moreover, perisarcal areas close to hydranths were more abundantly covered by algae, probably due to nutrient emission generated by the metabolism of the hydroid.

Dinoflagellates (Dinophyceae) are considered to be one of the most abundant and diverse groups of phytoplankton; however, the viral impact on dinoflagellates was not studied until recently. This review shows the present information concerning the viruses infecting dinoflagellates and the ecology relationships between the host and the virus. So far, two viruses have been isolated and characterized: a large DNA virus (HcV: Heterocapsa circularisquama virus) and a small RNA virus (HcRNAV: H. circularisquama RNA virus); both of which are infectious to the harmful bloom-forming dinoflagellate H. circularisquama.

In the present review, we mainly discuss the relationship between HcRNAV and H. circularisquama from the viewpoint of physiology, ecology and genetics. It will help clarify the viral impact on dinoflagellate populations in marine environments to understand the host/parasite ecology.

We report the occurrence of a high diversity of minute (∼1 μm diameter) organic and siliceous protistan scales in small samples (total volume ∼35 μl) of superficial sediment from the Porcupine Abyssal Plain (PAP), north-east Atlantic (4850 m water depth). Many exhibit characters by which they can be identified to species. The organic scales belong to the haptophyte genera Chrysochromulina (8–9 species), Chrysocampanula and Dolichomastix (1 species each). The siliceous scales belong to the chrysophytes Paraphysomonas vestita and Meringosphaera sp. and to the heterotrophic flagellate genus Thaumatomastix (T. dybsoeana, T. formosa, Thaumatomastix sp.). As far as we are aware, this is the first time that non-calcareous protistan scales have been observed in deep-sea sediments (although siliceous skeletal plates and cysts are reported). All scales probably originated from the upper water column and were delivered to the deep-sea floor on rapidly sinking detrital aggregates. However, naked heterotrophic flagellates are known to thrive in abyssal sediment habitats and so the possibility that some scale-bearing protists also live in benthic deep-sea environments cannot be eliminated. Many species identified at the PAP site are common in coastal marine waters around Europe; some occur as far afield as Tasmania and New Zealand. Five Chrysochromulina species are known from central oceanic areas, including parts of the North Atlantic, while another species, C. pringsheimii, is reported from a British freshwater lake. We retrieved ∼15% of the 55 named Chrysochromulina species (∼8% of the estimated total number of species in this diverse group) in the ∼35 μl of abyssal sediment. Because the scales can persist and be identified after cell death, they may provide useful time- and space-averaged information about the distribution of protist species in marine habitats. The long-term fate of the scales on the sea-floor is unknown. It is possible that at least some of the organic scales are preserved as microfossils in deep-sea sediments.

Four species of gymnamoebae isolated from a sandy shore were subjected to hydrodynamic disturbance within microcosms. Increasing the level of disturbance increased the generation times of all four isolates. Generation times of a small Platyamoeba sp. and a limax amoeba were least affected by increasing disturbance. The greatest increase in generation times was observed in populations of two large (>15 μm) Mayorella sp. and Vannella sp. This study shows that hydrodynamic disturbance may be an important community structuring force within natural marine amoebae communities.