This study evaluates the influence of man-made activities on the benthic environment at two different marinas: Southsea Marina on the south coast of England, and Minimes Marina on the Atlantic coast of France. We assessed the differences in: (1) sediment percentage organic matter, particle size and heavy metal concentration, using copper (Cu), cadmium (Cd), zinc (Zn) and lead (Pb) as contamination indicators; (2) sediment elutriate toxicity (LC50) using algal (Fucus serratus) bioassay; and (3) benthic community characteristics (number of species, abundance, most contributing species (SIMPER) and biotic index (AMBI)). Canonical correspondence analysis (CCA) was performed to relate the abundance of species to the environmental variables. At both marinas, we observed an increasing gradient of contamination from outside to the innermost sites. At both marinas, the lowest macrofaunal abundance was recorded at the innermost sites and differences in benthic community structure were observed between sites. At Southsea Marina, the cirratulids Tharyx marioni and T. killariensis and the cossurid Cossura pygodactylata dominated sites outside, while the opportunistic species Capitellides girardi dominated the innermost sites. At Minimes Marina, the cirratulid Streblospio shrubsolii was abundant outside and at the middle sites but was almost absent at the innermost sites. The biotic index—AMBI—indicated that sediments in the innermost sites were heavily disturbed at Southsea Marina and slightly to moderately disturbed at Minimes Marina. In Southsea, the AMBI was positively correlated to the sediment metal concentrations (Cu, Zn and Cd) and elutriate toxicity (LC50), while in Minimes the AMBI was positively correlated to the % of sediment fine particle and elutriate toxicity (LC50).

Predation has long been recognized as an important biological force driving community patterns in intertidal rocky shores throughout the world. Little is known, however, about the role of predation by mobile marine predators in shaping intertidal prey populations in Portuguese rocky shores. The abundance and population structure of crabs were assessed during nocturnal low-tides on two rocky shores to characterize potential predator species. To assess the effect of predation on intertidal species including limpets, barnacles and mussels, predator exclusion experiments using full cage, partial cage and no cage treatments, were set up for two months on two shores on the central Portuguese coast. Pachygrapsus marmoratus (Fabricius) and Eriphia verrucosa (Forsskål) were the most abundant crabs. Results from predator exclusion experiments suggested that predators do not exert a significant control on abundance of limpets, mussels or barnacles on the midshore during the experimental period. Despite the fact that these crabs are known to feed on the analysed prey, several factors may account for the observed absence of impact on prey abundance and these are discussed.

The baited remote underwater video technique (BRUVS) was used to compare fish assemblages at three sites with different habitat characteristics: sandy bank (SB), rock reef (RR) and degraded coral reef (DCR) in Port Essington, Garig Gunak Barlu National Park, Northern Territory, Australia. The Carangidae family dominated, representing 35% of all recorded fish. The highest species number was recorded at RR followed by DCR and SB. The highest total fish number was recorded at DCR followed by SB and RR. Fish assemblages from all three sites are clearly different at high confidence level, but still overlapping and higher overlapping was found between SB and RR. Fish assemblages at all three studied sites contained some coral-associated species, fish fauna was less rich compared to coral reefs in the mouth of the bay and fish assemblages were noticeably different from typical coral fish communities. None of the fish assemblages at studied sites were presented by the ‘pure’, single habitat-associated association of species—at all three sites fish communities were a mixture of fish with various habitat preferences. Reef-associated species have a larger proportion at DCR and at RR their habitat complexity was higher; still soft-bottom habitat fish make substantial fractions in fish assemblages at both DCR and RR. Similarly, fish usually identified as ‘reef associated’ were found in notable proportions on SB. Fish with wide distribution and low selectivity in habitat preferences comprised a significant part in fish assemblages at all studied sites. In this study the BRUVS technique worked well in the area where diving visual surveys were impossible to implement because of high water turbidity. Another advantage of this method is the non-impact nature of visual survey; they can be used in long-term monitoring of fish assemblages at reference sites.

Structural parameters of periphytic ciliate communities on a modified substrate were studied in Korean coastal waters during the period August–November 2007. In order to reduce the strong disturbances from tidal current and circulation in marine ecosystems, a modified slide method, named the polyurethane foam enveloped slide (PFES) system, was used to host ciliate communities. A total of 37 ciliate species, about half of which belong to the orders Hypotrichida and Cyrtophorida, were identified using living observation and silver impregnation method with this system. The sessile ciliates belonged to the orders Peritrichida and Suctorida, while the motile forms were represented primarily by the species of the orders Hypotrichida, Cyrtophorida and Pleurostomatida. The species diversity and evenness were significantly higher in the PFES system than those on the conventional slides (paired t-test: t = 2.384, 2.415; P < 0.05). Multivariate analysis revealed that the ciliate communities from both sampling systems had similar species composition, but represented significant differences in species distribution and temporal dynamics mainly due to the most dominant peritrich Zoothaminium duplicatum, which overly colonized the conventional slides. Results suggest that the PFES system is more effective than the conventional slide method for periphytic ciliate colonization with high species diversity, evenness and sensitive temporal dynamics mainly due to the reduction of disturbances from tidal current and circulation in marine ecosystems.

The aim of the present study was to characterize the external morphology and the orientation of burrows constructed by the mangrove crab Ucides cordatus. Data were obtained from two mangrove forests of similar vegetation dominance (Laguncularia racemosa) but differing in flooding heights. These mangroves were located near Barra de Icapara, Iguape City (SP), Brazil, (24°50′36″S–47°59′53′W). A total of 221 burrows were examined (120 on the high mangrove and 101 on the low mangrove). External morphology of the burrows was recorded by photographs for categorization and description. The directions of the burrow openings were recorded using a geological compass and the declivities of the ducts were measured with a clinometer. Females constructed 70.8% at Site A and 69.4% at Site B of the occupied burrows with the opening facing the margin of the river (P < 0.001), whilst males showed no significant difference in the burrow orientation (P > 0.05) at either site. In females, the tendency for burrow orientation possibly has a reproductive connotation as larval dispersal may be favoured and enhanced by the tides. Four groups of distinct tracks related to the morphotypes and developmental stages of U. cordatus were observed. No sediment constructions associated with the burrows were recorded for this species. Declivity of the burrows from juveniles was lower than from adults (P < 0.05), probably caused by the differential growth of the chelipeds in this species.

Diversity is one of the most frequently used attributes of ecological communities, and there is a long-standing discussion about their adequate use, calculus and interpretation. One of the most conspicuous and simple diversity estimators is species richness, but it has been criticized by recurrent pitfalls, which has biased comparisons and the testing of hypotheses. Otherwise, synthetic ecological indices of diversity are difficult to interpret due to the underlying complex or cryptic concepts. Most of the studies in soft-bottom macroinvertebrate communities trying to estimate species richness, have actually quantified species diversity as species density; the number of species per unit area. In the present study, the diversity of a tropical Pacific soft bottom community is analytically decomposed using two null models to assess species richness and evenness, and the slope of species–area curves to estimate species density. A declining trend of species richness was observed along a 2-year period and could be related to the cumulative effects of interannual environmental variability and fishing disturbance. The species–area relationship could be considered a good indicator of spatial heterogeneity, specifically to illustrate the depth gradient. Local abundance was negatively correlated with evenness, showing that high-density communities are the result of increases in abundance of a few dominant species. Here we demonstrate that seasonality, depth and abundance could explain diversity in soft-bottom macroinvertebrate communities of coastal waters and propose a robust procedure to survey diversity as a part of monitoring programmes of coastal management.

The distribution of abundance and biomass of prokaryotes, flagellates, ciliates and phytoplankton, were studied in five ponds of increasing salinity in the Sfax solar saltern (Tunisia) coupled with environmental factors. The results showed that abundance of eukaryotic microorganisms decreased with increasing salinity of the ponds whereas prokaryotes (heterotrophic bacteria and Archaea) were abundant in the hyper-saline ponds. Phototrophic picoplankton was found in a large range of salinity values (70 and 200‰). Phototrophic non-flagellated nanoplankton which dominated in the first sampled pond was substituted by phototrophic flagellated nanoplankton in the other ponds. Heterotrophic nanoplankton dominated in the crystallizer pond but its quantitative importance declined in the less saline ponds. Diatoms and dinoflagellates were the major contributors to phytoplankton abundance in the first ponds (>90% of total abundance). Ciliated protozoa were found in all the ponds except in the crystallizer in which prokaryotes proliferated. Oligotrichida and Heterotrichida were the most abundant ciliate groups. Overall, species richness decreased with salinity gradient. We propose a simplified diagram of the Sfax saltern's food web showing the dominant role of the microbial loop along the salinity gradient.

Interannual variability of the primary production in the middle Adriatic Sea for the period 1961–2002 was examined and correlated to the various atmospheric and oceanographic parameters. The sequential t-test analysis of regime shift (STARS) method and locally-weighted scatter plot smoothing (LOWESS) method were applied to the primary production, revealing the new regime with significantly different mean productivity ranging from 1980–1996. Moreover, this period with the highest primary production, consists of the two distinguished sub-periods: periods of increasing (1980–1986) and decreasing (1987–1996) primary production. Whereas in the first period the ecosystem was under the influence of warmer and nutrient richer Levantine Intermediate Water (LIW) intrusions into the Adriatic, in the second period, which started with a cold winter in 1987, the Eastern Mediterranean Transient (EMT) occurred. The EMT established a new circulation regime which prevented the LIW intrusions in the Adriatic, causing its reduced productivity. Reduced LIW inflow in the Adriatic was evidenced in the lower than normal sea temperature, salinity and oxygen concentrations below the thermocline depth. Precipitation and wind regime also arose as important local factors for the primary production variability. Our analysis connected the shifts in primary production with hemispheric and regional scale climate variations, and supports the hypothesis that atmospheric variability can trigger the ecosystem changes.

Two species of the genus Pseudopolydora, Ps. dayii, sp. nov. and Ps. antennata, were associated with gastropods on the south and south-east coasts of South Africa. Pseudopolydora dayii is characterized by prominent post-chaetal notopodial lobes on chaetiger 1 with very long chaetae, a prominent occipital tentacle, having hooded hooks that start on chaetiger 9, branchiae that start on chaetiger 6, stout hooks and lobes placed latero-posteriorly to the hooded hooks in posterior chaetigers. It is a surface-fouler and was found on several species of wild gastropods at four of the five sites sampled and from additional material from the south-west coast and on cultured abalone (Haliotis midae) at a farm on the south-west coast. Three individuals of Ps. antennata were found only with oysters at the easternmost site. This was the first record of this species outside of the Western Cape Province and it is possible that their association with the oysters was fortuitous.

The capture of crabs of the genus Callinectes is one of the oldest extractive activities practised by waterside communities, due to the abundance of brachyurans along the Brazilian coast. The present paper aimed to provide basic information on the population biology of C. sapidus and C. danae during the period of December 2003 to November 2004, in Babitonga Bay, Joinville, Santa Catarina. The size of the first maturation of C. danae was estimated as 7.1 cm in total carapace width for females, and as 8.6 cm for males. Fecundity of the 20 females of C. danae with carapace width from 7.0 to 11.0 cm varied from 618,667 to 811,267 eggs. Fecundity of C. sapidus was higher, with a median of 978,000 eggs per female, but carapace widths in this species were also larger, with the highest frequency of females attaining 19.01 cm on average. In both species, a tendency was observed for the egg mass to increase with size of females. The capture per unit of effort presented the lowest values in summer, while the largest values occurred from March, August and November. A total of 80 males and 117 females of C. sapidus were captured in the four collecting areas, with the largest abundances in Area III (45.18%), followed by Areas II, IV and I. The size of the first maturation of C. sapidus was estimated as 10.2 cm for females and as 9.0 cm for males. Fishing effort was in relative equilibrium for adult stock (males = 58.75% and females = 52.99%) and juveniles (males = 41.25% and females = 47.01%). The largest monthly rates of biomass of C. sapidus occurred from April to November, with a peak of capture in August, without significant differences in the participation of males and females.

Adults of Pseudopolydora rosebelae sp. nov. inhabit silty tubes on muddy bottoms in shallow water in southern Brazil, states of São Paulo and Rio de Janeiro. They are rare and extremely delicate, attaining 20 mm long for 55 chaetigers. The worms are distinctive by their colourful yellow and black pigmentation on the anterior part of body and palps, prominent transverse hood on the dorsal anterior edge of chaetiger 3, and lack of coloured respiratory pigment in blood. Of 12 examined individuals, all were females. Oogenesis is intraovarian; oocytes develop from chaetigers 14–15 to chaetigers 24–36. Recently laid oocytes were about 150 μm in diameter, with embryos and developing larvae found in capsules inside female tubes in March–June. Broods comprised up to 23 capsules with 400 propagules. Capsules were joined to each other in a string and each attached by a single thin stalk to the inner wall of the tube. Larvae hatched at the 4-chaetiger stage and fed on plankton. Pelagic larvae are unique among Pseudopolydora in having large ramified mid-dorsal melanophores from chaetiger 3 onwards. Competent larvae are able to settle and metamorphose at the 15-chaetiger stage, but can remain planktonic up to 18 chaetigers. They have one pair of unpigmented ocelli and three pairs of black eyes in the prostomium, unpaired ramified mid-dorsal melanophores on chaetiger 1 and on the pygidium, ramified lateral melanophores on chaetigers 5–10, prominent yellow chromatophores in the prostomium, peristomium, on dorsal and ventral sides of chaetigers and in the pygidium. Branchiae are present on chaetigers 7–10, and gastrotrochs are arranged on chaetigers 3, 5, 7 and 12. Provisional serrated bristles are present in all notopodia, and hooks are present in neuropodia from chaetiger 8 onwards. Two pairs of provisional protonephridia are present in chaetigers 1 and 2, and adult metanephridia are present from chaetiger 4.

We examined the tooth ultra-structure of harbour porpoises (Phocoena phocoena) from Scottish waters to determine whether the incidence of mineralization anomalies could be related to certain life history events (e.g. the achievement of sexual maturation) as well as other factors that affect the general health of the individual (e.g. persistent organic pollutant (POP) concentrations in blubber). Five distinct types of mineralization anomalies were recorded: accessory lines, marker lines, dentinal resorption, cemental disturbance and pulp stones and the occurrence of these anomalies was scored by sex, age and maturity state. Overall, the incidence of mineralization anomalies was high and tended to increase with age. Marker lines and accessory lines were the most commonly recorded anomalies while pulp stones were least frequent. Duplicate teeth (i.e. from the same individual) always showed the same pattern of anomaly occurrence.

Fitted binary generalized linear and additive models indicated that the presence of dentinal resorption, cemental disturbance and marker lines in harbour porpoise teeth increased with age, body length and maturity. Males displayed marker lines more frequently than females. Age was the best predictor of the incidence of dentinal resorption and cemental disturbance while age and sex were the best predictors of the incidence of marker lines. The time course of appearance of dentinal resorption and cemental disturbance suggests that their occurrence could be related to physiological stress linked to sexual maturation. Marker lines were found within growth layer groups which coincided with the beginning of weaning and sexual maturation, suggesting an association with these two major life history events. Accessory lines were found in most teeth and may be a normal characteristic of porpoise teeth or reflect regular events. Pulp stones appeared only in mature animals. We found no evidence that the presence of anomalies in teeth was significantly related to POP concentrations in the blubber.

The Magharees fishery (Brandon and Tralee Bays in south-west Ireland) is 495 km2 in extent, the majority of this area ≤20 m in depth. Since 1981 it has been occupied by a directed spider crab fishery yielding in some years all of the national catch of Maja brachydactyla. Maximum recorded landings were 336 t in 1999 and effort has numbered up to 10,000 pots annually. Increasing fishing capacity and declining opportunities have accentuated fishing effort on spider crab. This paper describes a catch census undertaken in the fishing season of March to August inclusive, 2000–2007 and a mark–recapture experiment, 2005–2007. A method of ageing the adult moult by attributing a chronology to the rate of erosion of the claw on the dactyl is introduced. Males migrated longer distances, moved into the fishery on a wider trajectory and demonstrated greater wear on the claw than females. Recapture rate of males was twice that of females. The conduct of the fishery changed in its 26 years in existence. Landings became more concentrated in the earlier months of the year and the recent summer fishery was characterized by fewer male captures. Larger males were quickly removed and none >140 mm carapace length survived in the fishery longer than one year.

Competition plays an important role in invasion dynamics. According to Elton's biodiversity and invasibility hypothesis, non-native species must be competitively superior to the resident species in order to successfully invade. An invader that is ecologically similar to a native species may cause intense interspecific competition as they both require the same resource. Furthermore, an increase in the density of an invading competitor may enhance the intensity of the competitive interaction, however, this may be reduced if the inferior competitor has a refuge that reduces the amount of time it is in direct contact with the superior competitor. In laboratory-based competition experiments between the non-native caprellid Caprella mutica and two ecologically similar native caprellids Caprella linearis and Pseudoprotella phasma, C. mutica successfully displaced both species from homogeneous artificial habitat patches after 48 hours. Patches that contained a refuge reduced the number of C. linearis being displaced but only when C. mutica was at a low density. Potentially aggressive interactions between C. mutica and the native C. linearis may have caused C. linearis to be displaced from the patches and could have caused significantly higher mortality of C. linearis compared to the controls. This is the first study to show that the non-native C. mutica has the ability to displace ecologically similar native species when the resource space is limited and when the density of C. mutica was significantly (10 times) lower than the density of C. linearis.

A new thecideide brachiopod species, Thecidellina meyeri, is described from the southern Lesser Antilles (Aruba, Bonaire, Curaçao), Caribbean Sea, with unique morphological characters which clearly separate it from all other described species of Thecidellina in the region. A virtually complete series of ontogenetic stages is recorded, providing insight into the plasticity of shell development during growth in thecideide brachiopods and offering a well-defined standard for comparison with fossil material. Study of the soft tissue suggests that T. meyeri is dioecious, which contradicts the idea of Thecidellina to be hermaphroditic. The limited distribution and the unexpectedly high species diversity within the genus Thecidellina in the Caribbean region support the idea of allopatric speciation due to limited dispersal ability.

The spatial and temporal variations of the microphytoplankton communities were examined during four oceanographic cruises conducted between July 2005 and March 2007 aboard the RV ‘Hannibal’. Water thermal stratification started in May–June, and a thermocline established at 20 m depth, but ranged between 25 m during July and more than 30 m during September. The high concentrations of chlorophyll-a were observed during the May–June semi-mixed conditions and were mainly correlated with the concentrations of phosphate, suggesting a potential limitation by this nutrient. The Bacillariophyceae were dominant in the coastal samples, whereas they declined in the offshore area, most likely due to silicate shortage. Cyanobacteriae developed over semi-mixed conditions and at the thermocline depth. Relatively constant abundance of dinoflagellates was observed during the sampling periods from the coast to the offshore area, mainly explained by the high diversity species of this group. The results suggest that some phytoplankton taxa are generally adapted to specific hydrological conditions, whereas the dinoflagellates did not seem to follow this trend. Our findings have important biogeochemical implications in relationship with the export fluxes of the particulate matter throughout the water column.

A comparison between the diet of the franciscana and the boto-cinza is presented through the proximate-composition and caloric value of their main prey. The fish Stellifer cf. rastrifer, Pellona harroweri, Anchoa filifera, Isopisthus parvippinnis and Trichiurus lepturus and the squids Loligo sanpaulensis and L. plei were analysed for water, protein, lipid and mineral contents and gross energy (GE). The fish are more important in the diet of the boto-cinza and squids are consumed mostly by the franciscana. Loligo sanpaulensis had the higher water content and protein was the largest fraction of the organic matter in all prey species. Squids presented greater GE values than fish. The data on prey composition and energy from this study are the first for these South American dolphins.

Jellyfish (Cnidaria: Scyphozoa) are increasingly thought to play a number of important ecosystem roles, but often fundamental knowledge of their distribution, seasonality and inter-annual variability is lacking. Bloom forming species, due to their high densities, can have particularly intense trophic and socio-economic impacts. In northern Europe it is known that one particularly large (up to 30 kg wet weight) bloom forming jellyfish is Rhizostoma spp. Given the potential importance, we set out to review all known records from peer-reviewed and broader public literature of the jellyfish R. octopus (Linnaeus) and R. pulmo (Macri) (Scyphozoa: Rhizostomae) across western Europe. These data revealed distinct hotspots where regular Rhizostoma spp. aggregations appeared to form, with other sites characterized by occasional abundances and a widespread distribution of infrequent observations. Surveys of known R. octopus hotspots around the Irish Sea also revealed marked inter-annual variation with particularly high abundances forming during 2003. The location of such consistent aggregations and inter-annual variances are discussed in relation to physical, climatic and dietary variations.

The cryptic invasion of the Asian macroalga Codium fragile (Suringar) Hariot ssp. fragile on north-eastern Atlantic shores has been long considered a classical example of a successful invader that has competitively displaced native congeners. Yet, the lack of quantitative information about morphologically similar native congeners, namely Codium tomentosum Stackhouse and C. vermilara (Olivi) Delle Chiaje, has hindered interspecific comparisons and ecological predictions. From September 2002 to 2005, we made extensive intertidal surveys on 12 northern and 26 southern rocky shores of the English Channel, specifically documenting the abundance, distribution and identity of Codium assemblages. On the north side of the English Channel, the native C. tomentosum and alien C. fragile were both sparsely distributed in intertidal pools in Devon. In contrast, the natives were absent from and the alien was locally abundant in shallow lagoons and rocky reefs around Bembridge and Whitecliff on the Isle of Wight. Finally, in the Channel Islands off the Atlantic coast of France, Codium spp. were abundant in pools and on low-shore emergent substrata with native species predominating. Patterns of distribution varied substantially among Guernsey, Jersey and Alderney, despite their close proximity. The regional variation in the algal distributions merits further investigation to determine whether the pattern is produced by: (1) anthropogenic activities and effects; (2) ecological interactions; (3) oceanographic factors; or (4) some combination of these.

Archinome storchi sp. nov. is described as the second species of the family Archinomidae. The specimens were collected from a hydrothermal vent site in 2212 m depth on the Pacific–Antarctic Ridge at 37° S. It differs from Archinome rosacea mainly in the position of the anus, the first appearance of branchiae and the length of the nuchal cirrus. Additional specimens of A. rosacea collected from hydrothermal vent locations in the North Fiji Basin and on the Mid-Atlantic Ridge were used for morphological comparison. A synoptic table of characters is given for A. rosacea and A. storchi sp. nov. together with a list of records for Archinomidae compiled from the literature.