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.

A benthic survey was carried out from November 1998 to December 1999 in the tidal flats of Bahía Samborombón (Río de la Plata estuary, Argentina), in order to study the population structure, growth and secondary production of Laeonereis culveri. The samples were collected monthly in two intertidal areas with different environmental characteristics (San Clemente Creek and Punta Rasa). Growth was analysed using computer-based methods of length–frequency data (ELEFAN), and the secondary production was estimated by Crisp's and Hynes & Coleman's methods. Laeonereis culveri were recruited throughout the year, with two main peaks during spring and autumn. The autumn cohort showed growth rate (K) of 2 in San Clemente Creek and 1.8 in Punta Rasa. The seasonal oscillation of growth pointed out that worms grow very slowly during winter months. The life span of this cohort ranged from 15 to 17 months. The spring cohort showed higher growth rates in both sampled areas (K=3.3 in Punta Rasa and 3.1 in San Clemente Creek), whereas the growth oscillation showed similar values to those of the autumn cohort. The lowest growth rate was found in January and the life span was 9.5 months. The annual mean biomass in San Clemente Creek was 5.44 g m−2, with a mean production of 40.8 and 43.8 g m−2 y−1, according to the method used, and a production/biomass (P/B) ratio of 7.5 and 8 y−1 respectively. In Punta Rasa, the annual mean biomass (2.69 g m−2) and mean secondary production (19.44 and 23.61 g m−2 y−1, according to the method used) were lower than in San Clemente Creek, nevertheless the P/B ratio (7.2 and 8.7 y−1) was similar. The high secondary production and P/B ratio observed suggest that L. culveri transfer an important biomass to higher trophic levels, pointing out the very important role that this polychaete plays in the energy flux of this coastal estuarine ecosystem.

Rhodoliths were collected in Esperance Bay,Western Australia, using a Van Veen grab from a bed that covered an area approximately 2.2 km2, in depths of 38 ±1 m. Rhodolith abundance (biomass per 0.1 m3), mean size (maximum diameter), and morphotypes were compared among the inshore margin, offshore margin, and middle area of the bed. Accelerator Mass Spectrometry was used to estimate ages of five free-living rhodoliths. Rhodolith taxa included Hydrolithon munitum, Lithothamnion sp., an unidentified Melobesiodeae (a Mesophyllum or Synarthrophyton) and possibly a species of Sporolithon, with lumpy, warty, and fruticose morphologies. The middle area of the bed had significantly greater abundance of rhodoliths than either margin. Biomass of warty rhodoliths was greater in the middle area of the bed whereas fruticose and lumpy rhodoliths had similar biomass across the bed. The <20 mm size-class was the most abundant and these rhodoliths may originate from fragmentation of larger individuals. Radiocarbon age estimates ranged between calibrated ages of AD1050 and modern, indicating that a proportion of living rhodoliths consisted of fossil rhodoliths that had been recolonized. The combination of coastal morphology, gently-sloping sea-floor, hydrodynamics, and rhodolith morphology was representative of rhodolith beds found elsewhere in the world.

We report the first complete genome sequence of the marine diatom-infecting, positive-sense single-stranded RNA (ssRNA) virus, Rhizosolenia setigera RNA virus (RsRNAV). The genome is 8877 nucleotides (nt), polyadenylated, lacking a cap structure, and has two large open reading frames (ORFs): ORF-1 (4818 nt), a polyprotein gene coding for replicases, e.g. RNA helicase, RNA-dependent RNA polymerase (RdRp); and ORF-2 (2883 nt), a polyprotein gene coding for structural proteins. The ORFs are separated by a 323 nt intergenic region (IGR), flanked by a 624 nt 5′-untranslated region (UTR) and a 229 nt 3′-UTR. The deduced amino acid sequences for ORF-1 and ORF-2 respectively show considerable similarities to the non-structural and structural proteins of a marine raphidophyte-infecting virus HaRNAV (Heterosigma akashiwo RNA virus). Phylogenetic analyses of concatenated amino acid sequences of RNA helicase and RdRp domains supported the monophyly of RsRNAV, HaRNAV and a marine protist-infecting virus SssRNAV (Schizochytrium single-stranded RNA virus) with moderate bootstrap values of 79–83%, but not at the family level, whilst their monophyly was only weakly supported (50–55%) in the phylogenetic tree based on RdRp whole domain. As a result, comparison of the genome organization and sequence suggests RsRNAV is not a member of any currently defined virus family. In the RdRp tree, the positive-sense ssRNA viruses infecting Stramenopiles (RsRNAV, HaRNAV and SssRNAV) and Alveolata (HcRNAV (Heterocapsa circularisquama RNA virus)) were categorized into phylogenetically distant clades, which suggests a host/virus coevolution. Our study supports the hypothesis that a diverse array of ssRNA viruses exists in marine environments.

Recent studies indicate that monothalamous (single-chambered) foraminifera are an important component of meiobenthic communities in the brackish, coastal waters of the Black Sea. The dominant taxa include Psammophaga and Vellaria, both of which are common in estuarine settings in other parts of the world. Here, we describe Tinogullmia lukyanovae sp. nov. from the Crimean and Caucasus regions of the Black Sea. The new species is several hundreds of microns in size. It is characterized by a more or less symmetrical, spindle-shaped to cylindrical, organic-walled test with two terminal apertural structures, usually in the form of rounded or more elongate, nipple-like projections. The protoplasm is finely granular and a nucleus is not visible. The new species typically occurs in well-oxygenated water at depths of a few tens of metres or less. A specimen from a 250-m deep site off the Caucasus coast, tentatively assigned to T. lukyanovae sp. nov., is of particular interest because it occurs at a depth where the bottom water is anoxic and sulphidic.

The effect of tidal emersion on the epifauna of three common British intertidal macroalgae, Cladophora rupestris (Chlorophyceae), Laminaria digitata (Phaeophyceae) and Fucus serratus (Phaeophyceae) was investigated. Tidally-induced migration of intertidal fauna is well documented, but the aim of this study was to determine the effect of algal complexity on the degree of change in epifaunal community structure between tidal states. The structural complexity of each algal species was determined by measuring the fractal dimension (D) of algal outlines (1.76, 1.23 and 1.11 respectively for the three species). In the case of L. digitata, a weighted value for D was used to take account of the varying morphologies of the holdfast, stipe and blade. The hypotheses tested were: (i) that increased algal fractal complexity is associated with increased abundance and diversity of associated epifaunal communities; (ii) that community composition is significantly reduced during emersion in intertidal algae (due to faunal migration); and (iii) that the degree of migration due to the receding tide is significantly reduced in more geometrically complex algae. Overall, faunal communities associated with C. rupestris were significantly more abundant and diverse than those associated with the other algal species investigated. No significant migration away from seaweeds was observed for any faunal taxon from any of the algal species studied during emersion. However, harpacticoid copepod abundance increased significantly on L. digitata at low tide. It is likely that these copepods were associated with the holdfast or underside of the lamina for protection from desiccation and the elements. This suggested an advantage associated with inhabiting low shore macroalgae during emersion compared with migration into the subtidal zone.

Two sympatric species earlier differentiated by means of starch gel electrophoresis within Polydora cf. ciliata from the Sea of Japan are here identified and their adult and gamete morphology are described and illustrated. One species bores into various shells and coralline algae while the other bores only into gastropod shells occupied by hermit crabs. Both species have the prostomium anteriorly incised to rounded, 0–4 eyes, the caruncle extending to the end of chaetiger 2, heavy falcate spines of chaetiger 5 with a lateral tooth, branchiae beginning on chaetiger 7, and the pygidium disc-like to cup-shaped with a dorsal gap to only an incision. Males of the two species differ in aggregations of spermatids. The more opportunistic borer, which occurs in a greater number of hosts, always has 8-cell-aggregations of spermatids. These worms are here referred to as P. calcarea. The other species, in which spermatids are always interconnected in tetrads, is here described as a new one, P. manchenkoi sp. nov. The two species also differ in that prominent brownish-yellow pigment appears on the posterior segments after fixation in formaldehyde in P. manchenkoi sp. nov. but not in P. calcarea. It is suggested that spermatid aggregates and spermatozoan morphology be included in future polychaete descriptions when possible.

This article reports on a new species originating from the northern Chilean fjord region, which argued for the resurrection of Cornulotrocha, here classified as a new subgenus of Clathria, for sponges with choanosomal acanthostyles, ectosomal quasidiactinal monactines and rosettes of palmate (an)isochelae. Clathria (Cornulotrocha) rosetafiordica sp. nov. was collected at 23 m depth at Quintupeu fjord (∼42°S), and is unique within this very large genus, in possessing rosettes of palmate anisochelae. The new species is compared to the only other known Clathria (Cornulotrocha), viz. C. (Cornulotrocha) cheliradians n. comb.; to the single other Clathria known with anisochelae, viz C. (Thalysias) dubia; to other crustose Clathria from southern South America, the subantarctic and Antarctic areas; and also to other sponges bearing rosettes; and is considered clearly distinct from all. The phylogenetic significance of rosettes is discussed, a likely adaptive value being discarded in view of the variable location of such structures in the distinct poecilosclerid taxa in which they occur.

A new virus that infects the harmful algal bloom-forming microalga Phaeocystis globosa was isolated from surface water in the English Channel off the coast of Plymouth, UK, in May 2001. Phylogenetic analysis of the DNA polymerase gene revealed the virus isolate, designated PgV-102P, belongs to the family Phycodnaviridae, a group of large double-stranded DNA viruses known to infect algae. Basic characterization of PgV-102P revealed it was a lytic virus with a relatively slow culture lysis period of 10-days. The genome size (176 kbp) and capsid diameter (98 nm) of PgV-102P fall at the bottom end of the range expected for phycodnaviruses. Interestingly, PgV-102P did not cluster with other P. globosa viruses; instead, it was more closely related to other prymnesioviruses that infect the marine prymnesiophyte Chrysochromulina brevifilum. We discuss the effectiveness of DNA polymerase as a diagnostic marker. Although it is ideal for determining what family or even genus an algal virus belongs to, it is clear that the DNA polymerase gene does not have sufficient resolution when looking for relationships within algal virus genera.

The impact of date-mussel fishery on substratum rugosity was evaluated at Capo Noli and Isola di Bergeggi (Savona, north-western Italian coast) in the summer of 2004. A new measure of substratum rugosity was used as a surface-dependent index of complexity. The results were compared between impact and control sites using two-way analysis of variance and suggested that the mussel fishery reduces substratum complexity.

Two alpha growth form species of boring sponges, Clionapocillopora sp. nov. and Cliona mucronata are described from coral reefs in the Mexican Pacific Ocean. Clionapocillopora sp. nov. is a light brown sponge containing tylostyles that measure 146×5 μm. Tylostyles are generally curved and have a globular or mucronated head, sometimes placed at some distance from the proximal end. In addition, straight, short and thick tylostrongyles and centrotylote oxea occasionally appear. Cliona mucronata is reported for the first time in the eastern Pacific Ocean. It is a red to red-orange sponge with two types of tylostyles, long and slender tylostyles, and short ensiform tylostyles. Both species have been found exclusively excavating corals of the genus Pocillopora. The boring activity of Clionapocillopora sp. nov. produces a network of galleries with mainly rectangular or polygonal chambers measuring from 0.7 to 2.4 mm in diameter, and C. mucronata produces a network of reticulate galleries with irregularly spherical or ovoid chambers 1.14×0.67 mm in diameter.

Between May of 2000 and July of 2001 a study aiming to determine the seasonal variation of syllid local population abundances was carried out. Samples were taken every second month and consisted of two replicates, each one being a quadrat 20 cm wide. After fixing, the samples were washed and the draining water was passed through a 1 mm sieve; then the syllids were identified and counted. For each replicate a number of ecological indexes were calculated, namely population density, number of species and Shannon's and Simpson's diversity indexes, computing mean values for each sample. In order to identify the most representative species of the taxocoenosis the Ci (constancy index, frequency of the species ranging from 0 to 1) and Di (dominance index, relative abundance ranging from 0 to 100 considering all the collected individuals) were computed for each one.

Analysis of the eight samples yielded 6548 individuals and 48 species belonging to the four subfamilies of Syllidae, of which Exogoninae and Syllinae were the most abundant and diverse. During the study period, the syllid taxocoenosis suffered dramatic changes. The abundance, that in May of 2000 was 33,375±775 individuals/m2, diminished to 2162.5±37.5 in September. After this date, the population density slowly increased. The number of present species evolved in a very similar way. Twelve species occurred in all the samples, although just six were abundant enough to yield Ci×Di products exceeding 5, thus being considered as good descriptors of the taxocoenosis. The variation of population density for most of these species more or less paralleled that of the total population of syllids. With regards to relative abundance, the taxocoenosis was always clearly dominated by Exogoninae species, especially by Salvatoria vieitezi, whose dominance scores always fluctuated around 45%. Syllis prolifera was the only important non-Exogoninae species in terms of dominance, although this parameter showed strong variation in this species.

Harmeria scutulata, a cheilostome bryozoan with a circum-Arctic distribution, is an important component of intertidal and shallow subtidal rock communities. In terms of numerical abundance, H. scutulata can reach over 50% of total individuals within Arctic bryozoan assemblages. It is an annual, fast-growing species that loses over 70% of interactions for space with other organisms. Uniquely for a bryozoan, the subcircular colonies have large zooids at the centre ringed by a marginal zone of up to six generations of small zooids. This pattern is shown here to be due to polymorphism, reflecting a functional differentiation between large, feeding zooids (autozooids) and small, non-feeding zooids that brood embryos (gonozooids). The switch from the budding of autozooids to gonozooids occurs more or less simultaneously around the circumferential growing edge of the colony and is irreversible. Colonies apparently produce embryos only near the end of the growing season. Strong wave action and/or ice scour during the winter months destroys most of the colony but it is inferred that some of the gonozooids, which are more thickly calcified than the autozooids, overwinter, surviving into the spring and releasing their larvae to found a new generation of colonies. A formal systematic redescription of H. scutulata is given.

In the present study 23 species of paraonids from western Mexico collected from the intertidal zone to the continental shelf of Baja California Sur, Guaymas, Sonora, and Petacalco, Guerrero are reported. Eight of these species are first recorded from the Mexican coast: Aricidea (Acmira) assimilis, Aricidea (Acmira) catherinae, Aricidea (Allia) ramosa, Aricidea (Aricidea) longicirrata, Aricidea (Aricidea) minima, and Levinseniaoligobranchiata; Aricidea (Aricidea) minuta and Cirrophorusarmatus are cited for first time from the Pacific. Two new species are described. Aricidea (Aricidea) petacalcoensis sp. nov. has bifurcate antenna on prostomium without nuchal grooves, tapering branchiae in chaetigers 4–13, modified neuropodial chaetae from chaetiger 21. Cirrophorus magdalenaensis sp. nov. has prostomium without antennae, eyes or nuchal grooves, banchiae from chaetiger 5, having ten pairs, notopodial modified chaetae bayonet-shaped.

A first record of the genus Aciculites in the Mediterranean Sea and the description of Aciculites mediterranea sp. nov. are here presented from a faunistic survey in a dark shallow marine cave of the north-western Sardinian karstic area. The new species is characterized by a massive cerebellum-like growth form, and a peculiar distribution of inhalant and exhalant areas, respectively, in depressed and elevated portions of the sponge surface. Oscules show a long narrow atrial cavity. Ectosomal skeleton is made of tangential anisostrongyles on elevated areas, and more or less vertical tufts of anisostrongyles in depressed inhalant areas. Anisostrongyles are smooth or with tips ornated by irregular tubercles. Sigmaspire microscleres are lacking. Choanosomal skeleton with tubercled irregular rizhoclone desmas and few scattered and variably oriented anisostrongyles. A comparative analysis of Aciculites mediterranea sp. nov. versus morphological diagnostic traits, geographical range and habitat of the species hitherto ascribed to Aciculites confirms that the peculiar distribution of the genus supports its relic condition of an ancient Tethyan fauna in the Mediterranean Sea.

Phytoplankton:virus interactions are important factors in aquatic nutrient cycling and community succession. The number of viral progeny resulting from an infection of a cell critically influences the propagation of infection and concomitantly the dynamics of phytoplankton populations. Host nucleotide content may be the resource limiting viral particle assembly. We present evidence for a strong linear correlation between measured viral burst sizes and viral burst sizes predicted from the host DNA content divided by the viral genome size, across a diversity of phytoplankton:viral pairs. An analysis of genome sizes therefore supports predictions of taxon-specific phytoplankton population density thresholds beyond which viral proliferation can trim populations or terminate phytoplankton blooms. We present corollaries showing that host:virus interactions may place evolutionary pressure towards genome reduction of both phytoplankton hosts and their viruses.

Cyanophage abundance has been shown to fluctuate over long timescales and with depth, but little is known about how it varies over short timescales. Previous short-term studies have relied on counting total virus numbers and therefore the phages which infect cyanobacteria cannot be distinguished from the total count.

In this study, an isolation-based approach was used to determine cyanophage abundance from water samples collected over a depth profile for a 24 h period from the Indian Ocean. Samples were used to infect Synechococcus sp. WH7803 and the number of plaque forming units (pfu) at each time point and depth were counted. At 10 m phage numbers were similar for most time-points, but there was a distinct peak in abundance at 0100 hours. Phage numbers were lower at 25 m and 50 m and did not show such strong temporal variation. No phages were found below this depth. Therefore, we conclude that only the abundance of phages in surface waters showed a clear temporal pattern over a short timescale. Fifty phages from a range of depths and time points were isolated and purified. The molecular diversity of these phages was estimated using a section of the phage-encoded psbD gene and the results from a phylogenetic analysis do not suggest that phages from the deeper waters form a distinct subgroup.

Eleutheria dichotoma, a hydrozoan not previously recorded from the southern hemisphere, was found at high densities at several locations along the coast of New South Wales (NSW), Australia, between August and November 2005. The identity of the species was confirmed by morphological and molecular (16S rDNA) comparisons with European specimens. Local densities, distribution and habitat (algal substrate) were examined. The medusae were found along a 400 km stretch of coastline between Bateau Bay (33°23′S 151°29′E) and Pebbly Beach (35°35′S 150°43′E), primarily on the green alga Ulva, at mean densities of more than 50 individuals per 10 cm2 plot. The species is probably a recent introduction to Australia.

This paper is concerned with comparing the relative performance of small (0.1 m2) and large (0.25 m2) Hamon grabs for sampling the benthic macro-invertebrates from coarse offshore marine sediments. We present results based on an actual survey near the Isle of Wight, UK, but we also summarize and develop a statistical theory as well as demonstrate the theory using a small simulation study. Our results show that: the larger grabs are more difficult to handle, especially from small vessels; for a given sampling area the small grab can provide a more precise estimate of abundance than the larger grab if the individuals are clustered; the smaller grab can detect more species than the larger grab if individuals from the same species are clustered together (in our study, approximately 5% more species); and the smaller grab may undersample larger macrofaunal species and also species that live on larger cobbles.

We present theoretical equations to demonstrate the two samplers abilities to capture cobbles of different sizes. Multivariate techniques suggest that differences in the composition of the fauna collected using the different sized grabs are statistically significant, but small. It is more expensive to process samples from the smaller grab per unit area. However, per grab, the smaller grab is cheaper. We also present a model to demonstrate the effect on species occurrence and abundance.

Prionospio patagonica inhabits temporary silty tubes intertidally and shallow subtidally in brackish water estuarine environments in southern Chile. The species is gonochoristic with the female:male ratio being close to 2:1. Females and males release gametes into water. Pelagic planktotrophic larvae were caught in the plankton in the River Valdivia estuary in October–November and in March. Development of the adult morphology is described and illustrated beginning from the 2-chaetiger larval stage. One pair of lateral eyes first appears in the early larva, and shortly after that the right median eye develops. The left median eye appears after settlement, in juveniles with 10–11 segments. Developed 6-segment larvae have three dark red eyes, short palps of equal length, no nototrochs, one pair of small cells with grasping cilia on the pygidium, a small ciliated pit, gastrotrochs on segments 2–6, long serrated bristles in notopodia, adult capillaries in noto- and neuropodia on segments 2–5, single hooks in both rami on segment 6, and one pair of provisional papillae on the pygidium. A ventral buccal bulb is present below the short oesophagus and two pairs of provisional protonephridia are present in segments 1 and 2. The wall of the anterior part of the midgut has a characteristic brown pigment. The 6-segment larvae, about 400 μm long, settle and undergo gradual metamorphosis. In adults, hooks are gradually lost from noto- and neuropodia but sabre chaetae appear from segment 7 and retain their anterior position as growth proceeds. Up to 14 pairs of cirriform branchiae develop from segment 2, and three adult cirri appear on the pygidium. The afferent and efferent arms of each branchial blood loop are interconnected by capillary loops. A greenish heart body is present in the main dorsal blood vessel in anterior segments. Up to 21 pairs of metanephridia develop in anterior sterile segments, beginning with segment 4. Transparent gonoducts are present in fertile segments.