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The giant clam Tridacna maxima has been largely overexploited in many tropical regions over the past decades, and was therefore listed in appendix II of the Convention of International Trade in Endangered Species (CITES) in 1985. In French Polynesia, several atolls and islands harbor the world's highest stocks of giant clams in very shallow and accessible areas, which are therefore highly vulnerable to fishing pressure. The local fishery authority (i.e., Direction des Resources Marines or "DRM") implemented several management schemes in 2002 to control and regulate fishing pressure. However, for further decisions DRM was missing a sensitivity analysis on the effectiveness of the possible management actions. Here, we report on the use of a deterministic Viable Population Analysis (VPA) and spatially-explicit age-based population model that simulated the 30-year trajectory of a Tridacna maxima stock under different management approaches. Specifically, given various scenarios of intra-island larval dispersal, we tested which of No-take-Areas (NTAs), rotational closures, size limits, quotas, and restocking schemes would lead to the highest future stocks in Tubuai and Raivavae, two exploited islands of the Austral archipelago. For both islands, stock abundances were estimated in 2004/2010 and 2005/2010 respectively, and natural mortalities were assessed previously only in Tubuai. When compared to field data, the model successfully predicted the 2010 stocks for Tubuai, but proved to be less reliable for Raivavae, where natural mortality rates may well be different from those on Tubuai. For Tubuai, the spatial model suggested that reducing fishing effort (through fixed quotas) and banning fishing below the 12 cm size limit (as currently implemented) were the most effective management actions to sustain T. maxima populations into the future. Implementing NTAs was of poor effectiveness. NTAs increased giant clam stock inside the protected area, but also increased overfishing in the neighboring areas, and were ineffective overall.

Small-scale spatial and temporal variability in animal abundance is an intrinsic characteristic of marine ecosystems but remains largely unknown for most animals, including coral reef fishes. In this study, we used a remote autonomous unbaited video system and recorded reef fish assemblages during daylight hours, 10 times a day for 34 consecutive days in a branching coral patch of the lagoon of New Caledonia. In total, 50 031 fish observations belonging to 114 taxa, 66 genera and 31 families were recorded in 256 recorded videos. Carnivores and herbivore-detritus feeders dominated the trophic structure. We found significant variations in the composition of fish assemblages between times of day. Taxa richness and fish abundance were greater in the early morning and in the late afternoon than during the day. Fourteen taxa displayed well-defined temporal patterns in abundance with one taxon influenced by time of day, six influenced by tidal state and seven influenced by both time of day and tidal state. None of these 14 taxa were piscivores, 10 were herbivore-detritus feeders, three were carnivores and one was plankton feeder. Our results suggest a diel migration from feeding grounds to shelter areas and highlight the importance of taking into account small-scale temporal variability in animal diversity and abundance when studying connectivity between habitats and monitoring communities.

The currents flowing across the rim of the atoll of Raroia were investigated with a 1 year-long dataset of wave, water level and currents. Offshore waves break on the edge of the reef outside the atoll's rim and drive current into the lagoon, through the shallow hoa that cut across the rim. The additional water volume generated by this wave driven flow induces an elevation of water level throughout the atoll's lagoon and is evacuated back into the open ocean through a deep reef pass. The water level inside the atoll is also driven by astronomical tides, which enter the lagoon thought the reef pass, after undergoing a ~50% decrease in amplitude and a ~4 hour lag. Using a simple parametric model with three calibrated coefficients, we show that currents across the atoll's rim can be estimated as a function of the offshore wave conditions and the water level difference between the ocean and the lagoon.

IndiSeas (>Indicators for the Seas>) is a collaborative international working group that was established in 2005 to evaluate the status of exploited marine ecosystems using a suite of indicators in a comparative framework. An initial shortlist of seven ecological indicators was selected to quantify the effects of fishing on the broader ecosystem using several criteria (i.e., ecological meaning, sensitivity to fishing, data availability, management objectives and public awareness). The suite comprised: (i) the inverse coefficient of variation of total biomass of surveyed species, (ii) mean fish length in the surveyed community, (iii) mean maximum life span of surveyed fish species, (iv) proportion of predatory fish in the surveyed community, (v) proportion of under and moderately exploited stocks, (vi) total biomass of surveyed species, and (vii) mean trophic level of the landed catch. In line with the Nagoya Strategic Plan of the Convention on Biological Diversity (2011-2020), we extended this suite to emphasize the broader biodiversity and conservation risks in exploited marine ecosystems. We selected a subset of indicators from a list of empirically based candidate biodiversity indicators initially established based on ecological significance to complement the original IndiSeas indicators. The additional selected indicators were: (viii) mean intrinsic vulnerability index of the fish landed catch, (ix) proportion of non-declining exploited species in the surveyed community, (x) catch-based marine trophic index, and (xi) mean trophic level of the surveyed community. Despite the lack of data in some ecosystems, we also selected (xii) mean trophic level of the modelled community, and (xiii) proportion of discards in the fishery as extra indicators. These additional indicators were examined, along with the initial set of IndiSeas ecological indicators, to evaluate whether adding new biodiversity indicators provided useful additional information to refine our understanding of the status evaluation of 29 exploited marine ecosystems. We used state and trend analyses, and we performed correlation, redundancy and multivariate tests. Existing developments in ecosystem-based fisheries management have largely focused on exploited species. Our study, using mostly fisheries independent survey-based indicators, highlights that biodiversity and conservation-based indicators are complementary to ecological indicators of fishing pressure. Thus, they should be used to provide additional information to evaluate the overall impact of fishing on exploited marine ecosystems. © 2015 Elsevier Ltd. All rights reserved We thank the Euroceans IndiSeas Working Group funded by the European Network of Excellence EUR-OCEANS (FP6, Contract N° 511106), the European collaborative project MEECE – Marine Ecosystem Evolution in a Changing Environment (FP7, Contract N° 212085) and IRD (Institute of Research for Development) and IOC/UNESCO. [...] MC was partially funded by the European Commission through the Marie Curie Career Integration Grant Fellowships – PCIG10-GA-2011-303534 – to the BIOWEB project and by the Spanish National Program Ramon y Cajal. LJS was supported through the South African Research Chair Initiative, funded through the South African Department of Science and Technology (DST) and administered by the South African National Research Foundation (NRF). LJS and YS were also funded by the European collaborative project MEECE – Marine Ecosystem Evolution in a Changing Environment – (FP7, Contract N° 212085). KMK was supported by the Northeast Fisheries Science Center and the Nature Conservancy through a grant from the Gordon and Betty Moore Foundation. MJJJ was supported by an EU Marie Curie International Outgoing Fellowship – PIOF-GA-2013-628116. MFB was supported by the Portuguese Oceanic and Atmospheric Institute and the trawl survey data collected under Biological Sampling (PNAB) Program. LJG would like to thank the Joint Research Centre of the European Commission for support. HO was financed by the Estonian Ministry of Education and Research (Grant SF0180005s10). JJH was supported by the Natural Environment Research Council and Department for Environment, Food and Rural Affairs [Grant Number NE/L003279/1, Marine Ecosystems Research Programme]. GIvdM was supported by the Institute of Marine Research, Norway. KT was partially funded by the project PERSEUS (Policy-oriented marine Environmental Research in the Southern EUropean Seas; FP7 Contract N° 287600). MAT was funded by the Spanish Institute of Oceanography (IEO) through a Predoctoral FPI fellowship. KNM was supported by a National Research Council fellowship at the Northwest Fishery Science Center. YJS and MTT were partially supported by the French project EMIBIOS (FRB, Contract No. APP-SCEN-2010-II). Chatham Rise trawl survey data were provided by the Ministry for Primary Industries. CL acknowledges DEVOTES – Development of innovative tools for understanding marine biodiversity and assessing good Environmental Status – EC project (FP7 Grant Agreement 308392) Coll, Marta ... et al.-- 16 pages, 6 figures, 6 tables Peer Reviewed

The diversity of cultivable methane-oxidizing bacteria (MOB) in the rice paddy field ecosystem was investigated by combined culture-dependent and fluorescence in situ hybridization (FISH) techniques. Seven microsites of a Japanese rice paddy field were the focus of the study: floodwater, surface soil, bulk soil, rhizosphere soil, root, basal stem of rice plant, and rice stumps of previous harvest. Based on pmoA gene analysis and transmission electron microscopy (TEM), four type I, and nine type II MOB isolates were obtained from the highest dilution series of enrichment cultures. The type I MOB isolates included a novel species in the genus Methylomonas from floodwater and this is the first type I MOB strain isolated from floodwater of a rice paddy field. In the type I MOB, two isolates from stumps were closely related to Methylomonas spp.; one isolate obtained from rhizosphere soil was most related to Methyloccocus-Methylocaldum-Methylogaea clade. Almost all the type II MOB isolates were related to Methylocystis methanotrophs. FISH confirmed the presence of both types I and II MOB in all the microsites and in the related enrichment cultures. The study reported, for the first time, the diversity of cultivable methanotrophs including a novel species of type I MOB in rice paddy field compartments. Refining growth media and culture conditions, in combination with molecular approaches, will allow us to broaden our knowledge on the MOB community in the rice paddy field ecosystem and consequently to implement strategies for mitigating CH4 emission from this ecosystem.

New Caledonia (Southwest Pacific), like all tropical Pacific Island countries, is impacted by weather events, climate change, and local anthropogenic forcing. Strong erosion of particles and dissolved organic matter (DOM) from ultramafic rocks, associated with trace metals dissemination (i.e., nickel, manganese and cobalt), potentially affects lagoon waters and coral reefs surrounding the main island. The CALIOPE (CALedonian Inherent Optical PropErties) cruises were performed along the Eastern Lagoon of New Caledonia (ELNC) (400 km, 13 transects from Bay to open ocean, 51 stations) during contrasted meteorological conditions: a dry period (October 2011), a windy situation (March 2014), and a strong rainy event (March 2016). CDOM absorption and fluorescence (FDOM), particulate absorption, backscattering, suspended particulate matter (SPM), total chlorophyll a (TChla), nutrients (NOx), pigment and phytoplankton composition were measured. Among the four CDOM fluorophores, the humic-like component (lambda(Ex)/lambda(Em): 235/460 nm), assimilated to a photoproduct of terrestrial organic matter, had relatively low fluorescence compared to protein-like fluorophores. As CDOM absorption, particulate absorption, backscattering, SPM, total chlorophyll a (TChla) and nutrient (NOx) concentrations, this humic-like material generally showed the highest values during rainfall events, the latter inducing an increase in riverine terrigeneous inputs and change toward higher phytoplankton size classes. The tyrosine 1-like (lambda(Ex)/lambda(Em): 220, 275/304 nm) and tryptophan-like fluorophores (lambda(Ex)/lambda(Em): 230, 300/352 nm) were strongly influenced by wind displaying a 7-fold and 3-fold increase, respectively in windy situation compared to calm conditions. These increases could be related to enhancements of autochthonous biological activities (highest mean concentrations of Synechococcus spp., phycoerythrin, pico- and nano-eukaryotes, heterotrophic bacteria and nanoplankton observed in wind condition) through the inputs of organic and mineral materials issued from the wind-induced sediment resuspension, atmospheric deposition and water mass mixing. By contrast, the tyrosine 2-like fluorophore (lambda(Ex)/lambda(Em): 245, 275/304 nm) substantially increased during rain events and presented the lowest values in wind conditions. These strong increases may be linked to the stimulation of planktonic activities due to riverine inputs. Therefore, this study emphasizes the significant differential influence of weather conditions (calm/wind/rain) on biogeochemistry and CDOM/FDOM distributions in the ELNC.

Le comportement trophique de l'anchois adulte (Engraulis encrasicolus) a été étudié dans le golfe du Lion (nord-ouest de la Méditerranée) en relation avec les facteurs environnementaux. Les observations ont été réalisées pendant la période majeure de reproduction (été) de deux années successives. Des profils hydrologiques, des pêches zooplanctoniques et des chalutages ont été effectués dans des zones caractérisées par de fortes densités d'anchois. La colonne d'eau est stratifiée en température, salinité et biomasse zooplanctonique, avec les cladocères nombreux au-dessus de la thermocline et les copépodes dominants au-dessous. L'anchois est strictement zooplanctonophage pendant la période majeure de reproduction se nourrissant essentiellement de copépodes et de larves de crustacés. Les anchois présentent une activité trophique importante au cours de la journée, lorsqu'ils se trouvent au-dessous de la thermocline, avec une ingestion de nourriture d'environ 4 % du poids frais de leur corps. Dans le golfe du Lion, l'anchois utilise deux types de mécanismes alimentaires : sélection sur les proies de grande taille et filtration sur les proies de petite taille. Feeding behaviour of adult European anchovy (Engraulis encrasicolus) was studied in the Gulf of Lions (northwestern Mediterranean Sea) in relation to major abiotic and biotic factors. Observations were made during the main spawning period (summer) for two years, data were collected through hydrological pro-tiling, zooplankton hauls and fish trawling performed in areas of high anchovy density. Temperature, salinity and zooplankton biomass were stratified in the study areas, with cladocerans numerous above the thermocline whereas copepods were dominant below. Engraulis encrasicolus was strictly zooplanctivorous during the main spawning season with copepod and crustacean larvae dominating in stomach contents. Anchovy exhibited high trophic activity during the day when they were below the thermocline, with food ingestion equivalent to about 4 % wet body weight per day. Anchovy in the Gulf of Lions employ two feeding modes: selective on large prey and filter-feeding mechanism on small prey.