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.

Biological Invasion of Fish Parasite Neoergasilus japonicus (Harada, 1930) (Copepoda: Ergasilidae) in Lake Grand Laoucien, France: A Field Study on Life Cycle Parameters and Reasons for Unusual High Population Density.

The fish parasite, Neoergasilus japonicus (Harada, 1930), native to Eastern Siberia and the Amur River catchment area, invaded European water bodies in the middle of the last century, possibly due to the human-mediated distribution of fish in the Amur complex (i.e., the genera Hypophthalmichthys and Ctenopharyngodon). In the deep karst lake, Grand Laoucien (Marseille area, France), this species had an unusually high population density (from 1000 ind./ m3 in zooplankton to 4000 ind./ m3 in the nearshore area) during the free-living period of its life cycle. The annual cycle of N. japonicus includes a 5-month overwintering of fertilized females attached to fish fins and, following this, a five- to six-generation chain from March to November, when the free-living stages in the population alternate with parasite females which attach to their hosts for breeding. The population density of the parasites in zooplankton increased exponentially from spring to autumn, which positively correlated with temperature. We found a strong correlation between N. japonicus density and the community development of microphytobenthos, but not between N. japonicus and phyto- or zooplankton dynamics. The local contributing factors included a seasonal three-fold decrease in water levels and the development of anoxia in profundal waters, which led to a high ambient fish density and thus susceptibility to the parasite. Although the free-living parasite represented only 1% of zooplankton production, it consumed up to 25% of small invertebrate productivity. The maximum intensity of infection reached 140 parasites per fish, or 4.14 per g of weight. The high infection of fish with this parasite, in our opinion, indicated the danger it poses to the local ichthyofauna, which first encountered this new parasite.

Male Differentiation in the Marine Copepod Oithona nana Reveals the Development of a New Nervous Ganglion and Lin12-Notch-Repeat Protein-Associated Proteolysis.

Copepods are among the most numerous animals, and they play an essential role in the marine trophic web and biogeochemical cycles. The genus Oithona is described as having the highest density of copepods. The Oithona male paradox describes the activity states of males, which are obliged to alternate between immobile and mobile phases for ambush feeding and mate searching, respectively, while the female is less mobile and feeds less. To characterize the molecular basis of this sexual dimorphism, we combined immunofluorescence, genomics, transcriptomics, and protein-protein interaction approaches and revealed the presence of a male-specific nervous ganglion. Transcriptomic analysis showed male-specific enrichment for nervous system development-related transcripts. Twenty-seven Lin12-Notch Repeat domain-containing protein coding genes (LDPGs) of the 75 LDPGs identified in the genome were specifically expressed in males. Furthermore, some LDPGs coded for proteins with predicted proteolytic activity, and proteases-associated transcripts showed a male-specific enrichment. Using yeast double-hybrid assays, we constructed a protein-protein interaction network involving two LDPs with proteases, extracellular matrix proteins, and neurogenesis-related proteins. We also hypothesized possible roles of the LDPGs in the development of the lateral ganglia through helping in extracellular matrix lysis, neurites growth guidance, and synapses genesis.

Investigating population-scale allelic differential expression in wild populations of Oithona similis (Cyclopoida, Claus, 1866).

Acclimation allowed by variation in gene or allele expression in natural populations is increasingly understood as a decisive mechanism, as much as adaptation, for species evolution. However, for small eukaryotic organisms, as species from zooplankton, classical methods face numerous challenges. Here, we propose the concept of allelic differential expression at the population-scale (psADE) to investigate the variation in allele expression in natural populations. We developed a novel approach to detect psADE based on metagenomic and metatranscriptomic data from environmental samples. This approach was applied on the widespread marine copepod, Oithona similis, by combining samples collected during the Tara Oceans expedition (2009-2013) and de novo transcriptome assemblies. Among a total of 25,768 single nucleotide variants (SNVs) of O. similis, 572 (2.2%) were affected by psADE in at least one population (FDR < 0.05). The distribution of SNVs under psADE in different populations is significantly shaped by population genomic differentiation (Pearson r = 0.87, p = 5.6 × 10-30), supporting a partial genetic control of psADE. Moreover, a significant amount of SNVs (0.6%) were under both selection and psADE (p < .05), supporting the hypothesis that natural selection and psADE tends to impact common loci. Population-scale allelic differential expression offers new insights into the gene regulation control in populations and its link with natural selection.

In situ heavy metals (copper, lead and cadmium) in different plankton compartments and suspended particulate matter in two coupled Mediterranean coastal ecosystems (Toulon Bay, France).

We monitored the concentrations of copper, lead and cadmium in seawater, in suspended particulate matter (SPM) and in bacteria, phyto- and zooplankton communities separated from abiogenic particles, over a one year cycle in two coupled Mediterranean coastal ecosystems (Little Bay (LiB) and Large Bay (LaB)). Metals were present in seawater in the order Cu>Pb>Cd in both bays and showed important variations within the same month than among months. In LiB, their concentrations were between 0.62 and 2.82 microg Cu l(-1), 0.16 and 19 microg Pb l(-1) and 0.007 and 0.14 microg Cd l(-1), respectively, whereas in LaB, they were between 0.23 and 2.11 microg Cu l(-1), 0.09 and 0.76 microg Pb l(-1) and not detected and 0.65 microg Cd l(-1). SPM play an important role on metal adsorption, especially for copper. Bioaccumulation factors showed that bacteria and phytoplankton accumulate metals whereas zooplankton tends to biodiminish them in the plankton food web.

Chitin distribution in the Oithona digestive and reproductive systems revealed by fluorescence microscopy.

Among copepods, which are the most abundant animals on Earth, the genus Oithona is described as one of the most numerous and plays a major role in the marine food chain and biogeochemical cycles, particularly through the excretion of chitin-coated fecal pellets. Despite the morphology of several Oithona species is well known, knowledge of its internal anatomy and chitin distribution is still limited. To answer this problem, Oithona nana and O. similis individuals were stained by Wheat Germ Agglutinin-Fluorescein IsoThioCyanate (WGA-FITC) and DiAmidino-2-PhenylIndole (DAPI) for fluorescence microscopy observations. The image analyses allowed a new description of the organization and chitin content of the digestive and reproductive systems of Oithona male and female. Chitin microfibrils were found all along the digestive system from the stomach to the hindgut with a higher concentration at the peritrophic membrane of the anterior midgut. Several midgut shrinkages were observed and proposed to be involved in faecal pellet shaping and motion. Amorphous chitin structures were also found to be a major component of the ducts and seminal vesicles and receptacles. The rapid staining protocol we proposed allowed a new insight into the Oithona internal anatomy and highlighted the role of chitin in the digestion and reproduction. This method could be applied to a wide range of copepods in order to perform comparative anatomy analyses.

Origin and characteristics of the zooplankton phosphatase activity in a coastal ecosystem of the Mediterranean sea (Toulon Bay).

In Toulon Bay (France), very high phosphatase activities have been found in the zooplankton fraction>90 microm. This work was intended to specify their origin. For that purpose, larvae, juvenile and adult Crustacea (Copepods: Calanoids, Cyclopoids, Branchiopods: Cladocera, and Cirripeds) were isolated. Their activities were measured using paranitrophenyl phosphate dissolved in sea water in order to calculate Km (the enzyme half saturation concentration) and Vmax (the reaction rate when the enzyme is saturated with substrate). Vmax were referred to protein contents of the isolated organisms to calculate specific activities. For all zooplankton groups high and low affinity phosphatase activities were found. The low affinity enzyme was responsible for at least 70% of the total phosphatase activity. Its specific activity was higher for larvae than for copepodites and adults. In Cirriped nauplii this activity was particularly high with values which were several hundred times higher than that in other Crustacea. These enzymes had optimum pH close to 8.4, magnesium requirement and were competitively inhibited by orthophosphate. Experiments with intact and lysed Cirriped nauplii confirmed that living organisms had only a weak external activity and showed that most of the activity of these larvae was primarily intracellular.

Role of DOP on the alkaline phosphatase activity of size fractionated plankton in coastal waters in the NW Mediterranean Sea (Toulon Bay, France).

The particulate material was fractionated into 5 size classes (>90µ, 50-90µ, 6-50µ, 1-6µ, and <1µ). DOP was analysed as easily (DOPh, DOPpa) and less easily hydrolysable compounds (DOPox). Based on Vmax, 94% of the high affinity AP activity was due to <50µ cells and 77% to <1µ cells. 83% of the low affinity activity was due to >90µ cells. The high affinity activities were negatively correlated with DOP for the <50µ classes. These correlations came mostly from DOPox. They were more significant when NO3+NO2 concentrations were high, when DIP concentrations were low and when N/P ratio was >10. At lower N/P ratios, AP was more significantly correlated with DIP. The low affinity activities showed significant negative correlation with DIP and with DOP and DOPox for the >90µ class. The inhibition of AP activities by DOPox may originate from stable compounds interfering with DIP for the control of AP synthesis.

Seasonal changes in phosphatase activities in Toulon Bay (France).

We studied the characteristics of the phosphatase activity (Km and Vmax) in total seawater and in particulate material of the three main plankton classes (0.25-5, 5-90 and >90 microm) in a coastal marine ecosystem of Toulon Bay (French Mediterranean Sea). The measurement of the hydrolysis of sodium paranitrophenylphosphate (pNPP), a substrate of phosphatase, revealed low and high affinity components in unfiltered seawater and in particulate matter. In unfiltered seawater, the low affinity activity was predominant from October to March during phytoplankton development. The high affinity activity dominated from April to June and was significantly correlated with the bacterial abundances. The phosphatase behaviour in the particulate material differs from that in the unfiltered seawater. The activity of the three particulate classes was generally much lower than that of unfiltered seawater, particularly the low affinity activity. The >90 microm size fraction consisted in greater part of zooplankton. In this size class, the activity (nmol l(-1) h(-1)) of the low affinity component was predominant from May to August, when the abundance of the larvae of copepods (copepodites) was highest. Its high specific activity (Activity/Protein concentration as nmol l(-1) h(-1) microg(-1)) was particularly elevated during this period. The 5-90 microm fraction consisted of phytoplankton cells, especially Dinoflagellates. Between September and January, the activity (nmol l(-1) h(-1)) of this size class was mostly supported by the low affinity component. The specific activity (nmol l(-1) h(-1) microg(-1)) of the high affinity component was highest in June and August. No significant correlation was found between phosphatase activities and chlorophyll a or total cell abundance. In return temporary relationships with specific taxa exist in particular with Ceratium spp., Gymnodinium spp. and Protoperidinium spp. The contribution of the 0.25-5 microm size class exceeded rarely 20% of the total particulate activity. Between June and August, high specific activities (nmol l(-1) h(-1) microg(-1)) were observed for its high affinity component. In autumn, strong rainfall increased the phosphate and nitrate concentrations and led to a drop in salinity, which probably explains the low phosphatase activities (nmol l(-1) h(-1)) and cell densities observed during this period.

Comprehensive model of annual plankton succession based on the whole-plankton time series approach.

Ecological succession provides a widely accepted description of seasonal changes in phytoplankton and mesozooplankton assemblages in the natural environment, but concurrent changes in smaller (i.e. microbes) and larger (i.e. macroplankton) organisms are not included in the model because plankton ranging from bacteria to jellies are seldom sampled and analyzed simultaneously. Here we studied, for the first time in the aquatic literature, the succession of marine plankton in the whole-plankton assemblage that spanned 5 orders of magnitude in size from microbes to macroplankton predators (not including fish or fish larvae, for which no consistent data were available). Samples were collected in the northwestern Mediterranean Sea (Bay of Villefranche) weekly during 10 months. Simultaneously collected samples were analyzed by flow cytometry, inverse microscopy, FlowCam, and ZooScan. The whole-plankton assemblage underwent sharp reorganizations that corresponded to bottom-up events of vertical mixing in the water-column, and its development was top-down controlled by large gelatinous filter feeders and predators. Based on the results provided by our novel whole-plankton assemblage approach, we propose a new comprehensive conceptual model of the annual plankton succession (i.e. whole plankton model) characterized by both stepwise stacking of four broad trophic communities from early spring through summer, which is a new concept, and progressive replacement of ecological plankton categories within the different trophic communities, as recognised traditionally.

Ocean plankton. Environmental characteristics of Agulhas rings affect interocean plankton transport.

Agulhas rings provide the principal route for ocean waters to circulate from the Indo-Pacific to the Atlantic basin. Their influence on global ocean circulation is well known, but their role in plankton transport is largely unexplored. We show that, although the coarse taxonomic structure of plankton communities is continuous across the Agulhas choke point, South Atlantic plankton diversity is altered compared with Indian Ocean source populations. Modeling and in situ sampling of a young Agulhas ring indicate that strong vertical mixing drives complex nitrogen cycling, shaping community metabolism and biogeochemical signatures as the ring and associated plankton transit westward. The peculiar local environment inside Agulhas rings may provide a selective mechanism contributing to the limited dispersal of Indian Ocean plankton populations into the Atlantic.

Seasonal changes in zooplanktonic alkaline phosphatase activity in Toulon Bay (France): the role of Cypris larvae.

We studied zooplankton contribution to the total particulate phosphatase activity, the kinetics of this activity, the relation to the different taxonomic groups and the role of particle-bound bacteria. The activity of total particulate material collected from a liter of seawater was more elevated in May, June and August than during the rest of the year. These high activities resulted from a high contribution of the >90 microm fraction which account then for more than 60% of the total particulate activity. Two Michaelian processes with high and low V(max) were disclosed on this fraction. The high V(max) component was responsible for the high summer activities. During these periods, high densities of cirriped Cypris were found which were statistically correlated with this high V(max) component as with its specific activity. Moreover, the contribution of attached bacteria to these high activities was low. In return, this contribution was predominant during the periods of low activity. A simple method was developed to characterise this bacterial activity.

Analysis of the role of DOP on the particulate phosphatase activity in Toulon Bay (N.W. Mediterranean Sea, France).

Alkaline phosphatase (AP) activity was studied on homogenates of particulate material in relation to the concentrations of AP-hydrolysable (DOPpa) and AP-non hydrolysable (DOPr) phosphorus. AP activity had high and low Km components. The high affinity activity came from ectoenzymes. It was negatively and significantly correlated with DOPr as with the sum of DIP and DOPr, but not with DOPpa. However negative correlations with DOPpa existed when DIP concentrations decreased. Significant correlations with the sum of DIP and DOPpa attest of additive effects of DIP and DOPpa. The low affinity activity came from "endoenzymes". This activity was also negatively correlated with DOP (DOPpa and DOPr). DOPpa and to a lesser extent DOPr influenced also positively the protein and/or Chlorophyll biomasses of the particulate material. We hypothesize that the correlations of the AP activity with DOP come from regenerated phosphate sequestered in cells and not released in the environment with DIP.

The relationships between particulate and soluble alkaline phosphatase activities and the concentration of phosphorus dissolved in the seawater of Toulon Bay (NW Mediterranean).

The activities of particulate and soluble phosphatase were analyzed monthly for 1 year in the coastal ecosystems of the NW Mediterranean Sea. The mean contribution of the particulate activity increased from 56% at an MUF-P concentration of 30 µM to 77% at 0.04 µM. This particulate activity was negatively correlated with the DIP, DOP and TDP concentrations when the activities were related to the seawater volume, chlorophyll a or the protein concentration. The TDP correlations were highly significant (p: 0.001). The DOP correlations were significant (p: 0.04) and became highly significant (p: 0.009) at low DIP concentrations (<0.13 µM). The DIP correlations were significant (p: 0.04) only at low DOP concentrations (<0.18 µM). Thus, the effects of seawater DIP and DOP were found to be linked. The soluble activity exhibited distinct phosphatase fractions with high (0.5-29.5 µM) and low (0.02-2 µM) Km values, but none exhibited significant correlations with phosphorus compounds.

Role of sea water DIP and DOP in controlling bulk alkaline phosphatase activity in N.W. Mediterranean Sea (Toulon, France).

The regulation of alkaline phosphatase activity by dissolved inorganic (DIP) and organic phosphorus (DOP) and the contribution of DOP as phosphorus source were studied monthly in Toulon Bay (NW Mediterranean, France) in 2005-2006. The concentrations of DIP and DOP varied respectively from 0 to 0.185µM and from 0 to 0.329µM. The bulk activities (Vm, Km, Vm/Km) were measured using MUFP as substrate. Its high affinity component (Km: 0.05-1.00µM) was negatively correlated with the sum of the concentrations of DIP and DOP but not with these compounds taken independently. A negative correlation with DIP was found when the concentrations of DOP were lower than 0.08µM. A negative correlation with DOP was shown when the concentrations of DIP were lower than 0.05µM. This high affinity component can be considered as a valuable indicator for the potential utilization of the compounds which contribute to the intracellular phosphorus pool.

Protein expression from zooplankton communities in a metal contaminated NW mediterranean coastal ecosystem.

Bidimensional and monodimensional polyacrylamide gel electrophoresis were used to study protein expression from zooplankton collected in thirteen stations of Toulon Bay (NW Mediterranean). In this ecosystem, Little Bay showed higher trace metal concentrations (13.5-23.8 nM for Cu, 0.73-1.24 nM for Pb, 27.8-58.7 nM for Zn) than Large Bay (Cu 2.2-15.6 nM; Pb 0.19-0.78 nM; Zn 9.0-38.8 nM). Trace metals positively correlated (p < 0.05) with expression of four zooplankton proteins (MW in kDa/pI: 25.0/5.6; 48.8/4.1; 38.2/4.4; 38.3/5.8) and with biomass of Oithona nana, predominant copepod in Little Bay. Sequencing by LC-MS/MS putatively provided zooplankton identity of these proteins: they were cytoskeleton actin, except one protein that was the chaperone calreticulin. We suggest that actin and calreticulin could be regarded as zooplankton markers of metal stress and be involved in a possible tolerance of O. nana to contamination, contributing to its development in a marine perturbed ecosystem.