New insights into global biogeography,population structure and natural selection from the genome of the epipelagic copepod Oithona

In the epipelagic ocean, the genus Oithona is considered as one of the most abundant and widespread copepods and plays an important role in the trophic food web. Despite its ecological importance, little is known about Oithona and cyclopoid copepods genomics. Therefore, we sequenced, assembled and annotated the genome of Oithona nana. The comparative genomic analysis integrating available copepod genomes highlighted the expansions of genes related to stress response, cell differentiation and development, including genes coding Lin12‐Notch‐repeat (LNR) domain proteins. The Oithona biogeography based on 28S sequences and metagenomic reads from the Tara Oceans expedition showed the presence of O. nana mostly in the Mediterranean Sea (MS) and confirmed the amphitropical distribution of Oithona similis. The population genomics analyses of O. nana in the Northern MS, integrating the Tara Oceans metagenomic data and the O. nana genome, led to the identification of genetic structure between populations from the MS basins. Furthermore, 20 loci were found to be under positive selection including four missense and eight synonymous variants, harbouring soft or hard selective sweep patterns. One of the missense variants was localized in the LNR domain of the coding region of a male‐specific gene. The variation in the B‐allele frequency with respect to the MS circulation pattern showed the presence of genomic clines between O. nana and another undefined Oithona species possibly imported through Atlantic waters. This study provides new approaches and results in zooplankton population genomics through the integration of metagenomic and oceanographic data.     

Population dynamics and production of the small copepod Oithona spp. in a subarctic fjord of West Greenland

The small cyclopoid copepod Oithona is widely occurring in polar areas; however, knowledge of its biology and ecology is very limited. Here, we investigate the population dynamics, vertical distribution, and reproductive characteristics of Oithona spp. from late winter to summer, in a subarctic fjord of West Greenland. During winter–early spring, the abundance of Oithona spp. was low (1.8 × 10³ ind. m^?2) and the population was mainly composed of late copepodites and adults, whereas in summer, abundance peaked and younger stages dominated (1.1 × 10⁶ ind. m^?2). In general, all stages of Oithona spp. remained in the upper 100 m, with nauplii exhibiting a shallower distribution. Although no general seasonal migration was found, a deeper distribution of the adult females in winter was observed. The mean clutch size of Oithona spp. varied from 16 to 30 eggs per female, peaking in summer. Egg production rates (EPR) were low in winter–early spring (0.13 ± 0.03 eggs female^?1 day^?1) and reached maximum values in summer (1.6 ± 0.45 eggs female^?1 day^?1). EPR of Oithona spp. showed a significantly positive relationship with both temperature and protozooplankton biomass, and the development of the population seemed to be appreciably affected by temperature. Oithona spp. remained active throughout the study, stressing the key importance of these small copepods in high-latitude ecosystems, especially in periods when larger copepods are not present in the surface layer.     

Interannual fluctuations in copepod abundance and contribution of small forms in the Drake Passage during austral summer

The relative importance of small forms of copepods has been historically underestimated by the traditional use of 200?C300-??m mesh nets. This work quantified the distribution and abundance of copepods, considering two size fractions (<300???m and >300???m), in superficial waters (9?m deep) of the Drake Passage and contributed to the knowledge of their interannual fluctuations among three summers. Four types of nauplii and eleven species of copepods at copepodite and adult stages were identified, with abundance values of up to 13 ind L^?1 and 28,300???g C m^?3. The <300-??m fraction, composed of Oithona similis, small cyclopoids and nauplii, dominated the copepod communities in the 3?years; it accounted for more than 77% of the total number and for between 40 and 63% of the total biomass. Changes in density and biomass values among the three cruises differed according to copepod size fraction and water mass; the >300-??m fraction showed no changes among the 3?years, both in Antarctic (density and biomass) and in Subantarctic waters (density), whereas the <300-??m fraction showed higher (density and biomass) values in 2001 both in Subantarctic and in Antarctic waters. Sea surface temperature and its anomaly accounted for the largest proportion of variability in copepod density and biomass, particularly for the <300-??m fraction.     

Seasonal variations in copepod body length: a comparison between different species in the Lagoon of Venice

The seasonal variation in length of the most abundant copepod species in the lagoon of Venice were compared and the relative influence of temperature, chlorophyll concentration and salinity examined. Temperature seems to be the primary factor influencing copepod body length in the lagoon of Venice, but the different species vary markedly in their response. Calanoid copepods (Acartia clausi, A. tonsa, Paracalanus parvus and Centropages ponticus) showed a more definite trend of size variation with temperature than the cyclopoids (Oithona nana and O. similis) and the harpacticoid Euterpina acutifrons. The size of the poecilostomatoids Oncaea media and O. subtilis was not affected by temperature, and was almost constant over time. Differences in the metabolic rates, longevity and specialization of calanoid, cyclopoid and harpacticoid copepods could explain their different responses to temperature.     

The mortality of the planktonic copepod <Emphasis Type="Italic">Oithona similis</Emphasis> Claus, 1866 (Copepoda: Cyclopoida) in the Barents and White Seas

The mortality rates of the copepodite IV-copepodite V and copepodite V-adult individuals pairs in the populations of one of the most common species of planktonic copepod, Oithona similis, were estimated for the first time in the Barents and White seas. The average parameters were 0.060 and 0.082/day, respectively, in the Barents Sea and 0.166 and 0.120/day in the White Sea. In the Barents Sea, the mortality rates of O. similis significantly increased with an increase in water temperature and in the White Sea a significant decrease occurred with an increase in salinity. It was concluded that the mortality rate of this species is determined first by abiotic factors and that biotic factors are of secondary significance.     

Seasonality of the copepod assemblages associated with interplay waters off northeastern Taiwan

This study investigated copepod assemblages in the regime around Turtle Island off northern Taiwan to trace South China Sea water (SCSW) flowing northward with the Kuroshio Current. Seasonal variations of copepod assemblages demonstrated a dynamic succession of changes in copepod populations; the average abundance for total copepods ranged from 102.58 ± 53.38 in December to 1669.89 ± 1866.17 in March (individuals m^?3). A total of 87 copepod species representing 36 genera and 21 families were identified. Among all samples, Temora turbinata dominated the copepods by a relative abundance (RA) of 26.89 %, followed by Paracalanus parvus (RA: 22.34 %) and Corycaeus (Ditrichocorycaeus) affinis (RA: 12.77 %). Only the Acrocalanus gracilis species was recorded in all samples. Results of one-way ANOVA revealed that the number of copepod species, indices of richness, evenness, and Shannon–Wiener diversity differed significantly in five different cruises. The density of five copepod species (Gaetanus minor, Calanus sinicus, Eucalanus elongates, Rhincalanus nasutus, and Rhincalanus rostrifrons) exhibited a significant negative correlation with seawater temperature. In contrast, the density of Canthocalanus pauper and Undinula vulgaris was significantly positively correlated with seawater temperature. The cold-water indicator species, C. sinicus, recorded in samples of March and May indicated the effect of China Coast Water (CCW) on copepod communities in the study area. Furthermore, the presence of Calanoides philippinensis in May samples strongly indicated that the SCSW may reach the Turtle Island area. Consequently, C. philippinensis and C. sinicus can be used to trace SCSW and CCW, respectively, in the study area.     

The zooplankton community in bays of Toulon area (northwest Mediterranean Sea,France)

The abundance and the diversity of the zooplankton community were studied during an annual cycle in three shallow bays differently affected by anthropogenic inputs of Toulon area in the northwest Mediterranean Sea (France). Environmental variables of water quality were also considered. Our results discriminated Little Bay from the La Garonne and Niel Bay. Little Bay, heavely perturbed by anthropogenic inputs, had high chlorophyll a levels, abundant zooplankton, a low diversity index, a high dominance Index and a single dominant species (Oithona nana). La Garonne Bay and Niel Bay, much less polluted, had low chlorophyll a levels, low zooplankton abundance, low dominance Index and high diversity index and eveness. In addition, O. nana occurred rarely in the latter bays. Zooplankton successions were also different between Little Bay and the two other bays.     

The seasonal abundance and production of Oithona nana (Copepoda:Cyclopoida) in Southampton Water

Recent studies indicate that Oithona spp. contribute significantlyto total copepod biomass. Little is known, however, about theirecological significance, particularly in the case of the estuarineOithona nana. A study comprising three sites within SouthamptonWater was conducted to evaluate the late-stage copepodite/adult(stages IV–VI) O. nana community, using 120-µm meshnets. Although present throughout the estuary, there was a strikingspatial gradient with O. nana most common in the upper estuary.A clear seasonal pattern was observed with O. nana as the mostabundant copepod species from late summer until early winter.It comprised 61% of all copepods recorded, with a biomass of757.22 mg C m^–3. Production estimates of O. nana werederived from the ‘instantaneous-growth’ approach,using appropriate growth equations. The estimated productionof O. nana ranged from 1.50 mg C m^–3 year^–1 withinthe lower estuary to 146.77 mg C m^–3 year^–1 in theupper estuary. In the upper estuary, this compares with productionrates of 187.47 mg C m^–3 year^–1 for all Acartiacongeners (excluding nauplii), the most common calanoid genus.Throughout the estuary, O. nana annual production represented18% of total copepod production clearly indicating that, atleast in the upper estuary, O. nana production may be directlycomparable with calanoid production.     

Seasonal variation in the distribution and abundance of Oithona and Oncaea species (Copepoda,Crustacea) in the southeastern Weddell Sea,Antarctica

The coupling between the seasonal distribution of dominant Oithonidae and Oncaeidae and the prevailing environmental conditions in the eastern Weddell Sea was investigated. In samples from February, a community on the shelf and in the oceanic surface layer, consisting mainly of Oithona similis and Oncaea curvata and juveniles of both genera, could be differentiated from a community found in deeper oceanic waters, consisting of Oithona frigida, Oncaea parila, Oncaea antarctica and Oncaea englishi. In November the differences in the species distribution between the two regions were less pronounced and the abundances of all species were much lower than earlier in the year. The dominant species were Oithona similis, which reached abundances of up to 182/m³ in February, and Oncaea curvata with up to 215/m³. Deeper living species were comparatively rare. Oithona similis occurred mainly in the top 200 m during both seasons. The other species, by contrast, were generally deeper and more dispersed through the water column in late winter than in summer.     

Distribution and dietary relationships of the Japanese temperate bass Lateolabrax japonicus juveniles with two contrasting copepod assemblages in estuarine nursery grounds in the Ariake Sea, Japan

Early juvenile Japanese temperate bass Lateolabrax japonicus samples were collected during four cruises to study the spatial and temporal patterns of distribution and feeding habits of the fish in Chikugo estuary, Ariake Sea, Japan. Gut contents were studied by separating, identifying and counting the prey organisms. Plankton samples were collected during each cruise to study the numerical abundance of copepods in the water. Copepod dry biomass and gut content dry mass were estimated. Juveniles were distributed over wide estuarine areas in salinities ranging from as low as 0·37 to as high as 28·81. Considerable spatial and temporal variations were observed in the copepod distribution in the environment and in the food habits of the fish. Two distinctly different copepod assemblages were identified along the estuary: one in the upper river, dominated by a single species Sinocalanus sinensis, and the other a multi‐specific assemblage in the lower estuary dominated by common coastal copepods such as Acartia omorii, Oithona davisae, Paracalanus parvus and Calanus sinicus. The gut content composition corresponded strongly with the copepod composition in the environment, i.e. a single species (S. sinensis) dietary habit at the upper river and a multi‐specific dietary habit dominated by the common coastal copepods in the lower estuary. Ivlev's electivity index showed that the fish strongly preferred larger copepods and avoided smaller ones. Higher dry biomass of copepods in the water as well as higher dry masses of the gut contents were recorded in the low‐to‐medium saline upper river areas, indicating that these areas are of particular importance as nursery grounds for the juvenile Japanese temperate bass. It was speculated that ascending to the upstream nursery areas to utilize S. sinensis, which is the single dominant copepod in these areas, is one of the most important survival strategies of the Japanese temperate bass juveniles in the Chikugo estuary.     

Artspezifische Merkmale der Faeces von vier dominierenden Copepodenarten der Kieler Bucht

Zusammenfassung 1. Die Kotballen der planktischen CopepodenartenAcartia bifilosa, Centropages hamatus, Oithona similis undPseudocalanus elongatus werden in ihrer Form, Länge und Breite beschrieben.2. Die aus Länge, Breite und Grundform der Faeces berechneten durchschnittlichen Volumina liegen zwischen 13 × 10³ µm³ für beide Geschlechter der ArtOithona similis und 348 × 10³ µm³ für die Kotballen der Weibchen der ArtAcartia bifilosa.3. Die Dimensionen der Faeces der vier untersuchten Arten zeigen in mindestens einem der untersuchten Parameter signifikante Unterschiede. Im Falle der ArtenAcartia bifilosa undCentropages hamatus sind auch die Größen der Kotballen beider Geschlechter signifikant verschieden.4. Ein Vergleich von Labor- und Freilanduntersuchungen zeigt, daß die in sedimentiertem Seston gefundenen Faeces planktischer Copepoden sich mit Hilfe der experimentell gefundenen Charakteristika den dominierenden Arten zuordnen lassen.

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Species-characteristics of the fecal pellets of four dominating copepod species of Kiel bight

Mean length, width and shape of the fecal pellets of the four planktonic copepod species,Acartia bifilosa, Centropages hamatus, Oithona similis andPseudocalanus elongatus, were studied. Mean volumes of the fecal pellets of the different species vary between 13 × 10³ µm³ (males and females ofOithona similis) and 348 × 10³ µm³ (females ofAcartia bifilosa). The dimensions of the fecal pellets of the four species examined reveal significant differences in at least one of the criteria studied. InAcartia bifilosa andCentropages hamatus even the length and width of the fecal pellets of the two sexes are different. With respect to the characteristics described, a comparison made between fecal pellets found in cultures with those obtained from sediment of the Baltic Sea (Kiel Bight) has shown that the latter may be attributed to the copepod species under consideration.

     

Copepod community structure and abundance in a tropical mangrove estuary,with comparisons to coastal waters

Zooplankton, sampled at five stations from the upper Sangga estuary (7 km upstream) in Matang Mangrove Forest Reserve (MMFR), Malaysia, to 16 km offshore, comprised more than 47% copepod. Copepod abundance was highest at nearshore waters (20,311 ind m⁻³), but decreased toward both upstream (15,572 ind m⁻³) and offshore waters (12,330 ind m⁻³). Copepod abundance was also higher during the wetter NE monsoon period as compared to the drier SW monsoon period, but vice versa for copepod species diversity. Redundancy analysis (RDA) shows that copepod community structure in the upper estuary, nearshore and offshore waters differed, being influenced by spatial and seasonal variations in environmental conditions. The copepods could generally be grouped into estuarine species (dominantly Acartia spinicauda Mori, Acartia sp1, Oithona aruensis Früchtl, and Oithona dissimilis Lindberg), stenohaline species (Acartia erythraea Giesbrecht, Acrocalanus gibber Giesbrecht, Paracalanus aculateus Giesbrecht, and Corycaeus andrewsi Farran) and euryhaline species (Parvocalanus crassirostris Dahl, Oithona simplex Farran, and Bestiolina similis (Sewell)). Shifts in copepod community structure due to monsoonal effects on water parameters occurred at the lower estuary. Copepod peak abundance in mangrove waters could be associated with the peak chlorophyll a concentration prior to it. Evidence of copepod consumption by many species of young fish and shrimp larvae in the MMFR estuary implies the considerable impact of phytoplankton and microphytobenthos on mangrove trophodynamics.     

Vernal abundance,structure and development of epipelagic copepod populations of the eastern Weddell Sea (Antarctica)

Summary Pelagic copepod populations under the pack ice of the Antarctic Weddell Sea were sampled with a 50 m net between October 2 and December 7, 1986, to study their abundance and developmental stage composition before and at the onset of the vernal phytoplankton bloom. Subadult stages and adult females were incubated to estimate rates of development and egg production. Copepod densities in the upper 200 m were highest for the small-sized species Oithona similis, Oncaea curvata and Ctenocalanus citer. About 95% of the copedite stages belonged to these species, dominated by Oithona. The copepodids were outnumbered by the nauplii in all species, except in Oncaea. The stage distribution in the small-sized species was bimodal with peaks in N3 and C4. The larger species Calanus propinquus and Metridia gerlachei showed peaks in nauplii only. Eggs were relatively abundant in all small and large species. Animals smaller than 1 mm not only were more abundant than the larger ones, but also had a higher total potential respiration. Eggs were produced by incubated females in sea water virtually without food at 0°C. Eggs hatched, and Oithona nauplii developed at a rate of about 7 days per stage. Copepodite stages did not develop significantly. Reproduction in the most abundant species commonly occurred before the algal spring increase when food levels were very low. Maintenance of a stable stage distribution at the expense of a high juvenile mortality seemed to be characteristic for the overwintering strategy of Antarctic copepods.     

Life histories of the copepods Pseudocalanus minutus, P. acuspes (Calanoida) and Oithona similis (Cyclopoida) in the Arctic Kongsfjorden (Svalbard)

The year-round variation in abundance and stage-specific (vertical) distribution of Pseudocalanus minutus and Oithona similis was studied in the Arctic Kongsfjorden, Svalbard. Maxima of vertically integrated abundance were found in November with 111,297 ind m⁻² for P. minutus and 704,633 ind m⁻² for O. similis. Minimum abundances comprised 1,088 ind m⁻² and 4,483 ind m⁻² in June for P. minutus and O. similis, respectively. The congener P. acuspes only occurred in low numbers (15–213 ind m⁻²), and successful reproduction was debatable. Reproduction of P. minutus took place in May/June, and stage distribution revealed a 1-year life cycle with copepodids CIII, CIV, and CV as the overwintering stages. Oithona similis exhibited two main reproductive peaks in June and August/September, respectively. Moreover, it reproduced more or less continuously throughout the whole year with all stages occurring during the entire sampling period, suggesting two generations per year. Both species migrated towards greater depth in November, but O. similis preferred to stay longer in the upper 100 m as compared to Pseudocalanus. The reproduction of the two species in Kongsfjorden seemed to be linked to phytoplankton dynamics.     

Variability of morphological characteristics in <Emphasis Type="Italic">Oithona similis</Emphasis> (Copepoda: Cyclopoida) in the White Sea

The spatial variability of the body size and morphological structures of the planktonic copepod Oithona similis in the White Sea was studied. From north to south, there was a tendency for the male cephalothorax length to decrease. In moving from the central to the northern part of the sea and from the eastern to the western part, the relative antennule length in both sexes increased. The average body size of copepods was positively and the absolute (and relative) lengths of the antennules were negatively correlated with water salinity. The morphological variations have adaptive significance and are determined by environmental factors.     

Spatio-temporal distribution of Oithona similis in the Bornholm Basin (Central Baltic Sea)

Oithona similis is an abundant but poorly studied cyclopoidcopepod in the brackish Central Baltic Sea. We describe thespatio-temporal distribution of O. similis in a Central Balticdeep basin (Bornholm Basin) during spring and summer 1999. Usingvertically resolving sampling in parallel with hydrographicmeasurements, we found the copepod to dwell in the permanenthalocline characteristic of a Central Baltic deep basin. Thehabitat of O. similis is thus limited from above by low salinityand from below by low oxygen conditions, both characteristicfor the area. Horizontally resolving sampling yielded abundancesurfaces which were compared by analysis of variance showingsimilar patterns among sampling dates. Comparison with flowfields from a three-dimensional hydrodynamic model suggeststhat the horizontal distribution is primarily the result ofcirculation in the dwelling depth. The study shows how the physicalenvironment in the area determines the spatial distributionwhich might affect abundance and production of this copepod.     

Heavy Metals in Mussels (Mytilus galloprovincialis) from Marmara Sea, Turkey

Marmara Sea is one of the main catching areas of mussels (Mytilus galloprovincialis) in Turkey, and a significant portion of the harvest has been exported mainly to European countries. In this study, Zn, Cu, Cd, Hg, and Pb in mussels from ten catching areas in Marmara Sea were analyzed to investigate health risks associated with consuming mussels. Mercury was not detected (<0.15 ppb) in any of the samples. The highest concentrations of Cu and Cd were 3.473 and 0.740 mg kg^?1 (wet weight, WW), respectively, well below the maximum permissible levels. All samples contained Zn higher than 50 mg kg^?1, while Pb was above the limits in the samples from stations 1, 4, 6, and 8. Mussels from Marmara Sea are safe regarding Cu, Cd, and Hg but may contain Zn and Pb above the permissible limits. However, metal contents of mussels from Marmara Sea are mostly lower than those of the regions in other areas of the world. It was concluded that Marmara Sea has a potential of being a safe source of mussels if industrial inputs somewhat reduced and controlled. Concentrations of heavy metals in mussels must be monitored comprehensively and periodically with respect to the consumer health.     

Mesozooplankton structure in Dolgaya Bay (Barents Sea)

The community structure of mesozooplankton was investigated in Dolgaya Bay (southern Barents Sea), a subarctic fjord, using a Juday net (0.168-mm mesh size) in July, 2008. A total of 39 species and higher taxa were found. Average abundance, biomass and diversity (±standard error) were 153,403 ± 15,855 ind m⁻², 570 ± 61 mg dry mass m⁻², and 2.25 ± 0.09, respectively. Copepods were the most numerous species. The mesozooplankton communities were dominated by omnivores (Oithona similis and Acartia spp.). Vertical distribution of the mesozooplankton was characterized by copepod dominance at each sampled layer. There were no significant correlations among physical variables and biological parameters, except negative correlation for the mean biomass and mean water temperature.     

Diel distribution of copepods across a channel of an overwash mangrove island

The distribution of copepod species and their nauplii was studied in a narrow, blind channel on an overwash mangrove island offshore of Belize. Copepodids were sampled with a pump at five stations across the channel during a diel cycle. Diel changes of copepodid stages II – VI were marked by horizontal dispersal of Dioithona oculata, the dominant species, from swarms in the prop roots along the shore during the day to the edge of the prop root habitat at night. Migration of copepodids back to the prop roots appeared to be controlled endogenously because change from a night to a daytime age structure began before first light. Mean copepodid stage at subsurface depths in the channel and prop root edge decreased from 4.2 (with 6.0 = all adults) to 2.9 at predawn to 1.1 during day. The oceanic Oithona nana and O. simplex, and the coastal zone O. fonsecae were evenly distributed with depth and distance from shore during day and night, with avoidance of prop root shoreline during day. These species were much less abundant than Dioithona oculata in the prop roots, but of comparable or greater abundance in the channel. Coastal zone Acartia spinata exhibited evidence of swarming. Nauplii, sampled with a 25m plankton net, were dominated by harpacticoid (50%) and cyclopoid (34%) nauplii, which generally were more abundant at 1m than at the surface and more abundant at night than the day. Lagrangian current measurements indicated velocities at ebb tide twice those of flood tide (1.9 vs. 0.8 cm s^–1) and a minimal residence time of 5 days, which could result in advection of D. oculata nauplii out of the Lair Channel before their recruitment into swarms as copepodid stage II. Previously reported maximum swimming speeds of swarming D. oculata copepodid stages (2.0 cm s^–1) and greater densities in prop roots and near the benthos may help copepodids avoid advection. The swarming behavior and diel horizontal migration (or dispersal) reported for D. oculata appears analogous to that of limnetic zooplankton, which may swarm among macrophytes along shorelines during the day to avoid visual predators and disperse or migrate away from the shoreline at night.     

Some population parameters of Ruditapes philippinarum (Bivalvia,Veneridae) on the southern coast of the Marmara Sea,Turkey

Ruditapes philippinarum, a venerid clam, is a dominant species in the sandy and muddy areas in the coastal waters of the Marmara Sea. Intensive commercial harvesting of this species is conducted in these regions. We studied the population dynamics of R. philippinarum on the southern coast of the Marmara Sea (Band?rma). Samples were collected on a monthly basis between September 2012 and August 2013. Seasonal von Bertalanffy growth parameters using the length–frequency distribution of R. philippinarum were estimated at L _∞ = 67.50 mm and K = 0.33 year^?1, and the seasonal oscillation in growth rate was 0.53. The slowest growth period was in January. The growth performance index and potential lifespan were 3.182 and 8.06 years, respectively. The growth relationship was confirmed to have a positive allometric pattern. The average total mortality rate was estimated to be 0.777 year^?1, whereas the natural and fishing mortality rates were 0.539 and 0.238 year^?1, respectively. The current exploitation rate of R. philippinarum was 0.306. The recruitment pattern peaked during June–August, and spawning occurred between May and August. The results of this study provide valuable information on the status of R. philippinarum stocks.