Résumé: Preliminary studies conducted on the human gastro-intestinal tract have revealed that enteric viral communities play a preponderant role in microbial homeostatis. However to date, such communities have never been investigated in the fish gut. Herein, we examined the main ecological traits of viruses in the digestive tract of a euryhaline fish, the tilapia Sarotherodon melanotheron. Individuals were collected at 8 different sites in Senegal covering a salinity gradient from 3 to 104 parts per thousand, and showing large disparities in their organic pollutant concentrations. Results showed that the gut of S. melanotheron is home to a highly abundant viral community (0.2-10.7 x 10(9) viruses ml(-1)), distinct from the surrounding water, and essentially composed of phages of which a substantial proportion is temperate (the fraction of lysogenized cells-FLC ranging from 8.1 to 33.0%). Also, a positive and significant correlation was detected between FLC and the concentrations of polycyclic aromatic hydrocarbon in sediment, while no clear relationships were found between salinity and any of the microbial parameters considered. Finally, our data suggest that virus-bacteria interactions within the fish intestine are likely sensitive to the presence of particular xenobiotics, which may compromise the balance in the gut microbiota, and subsequently affect the health of their host.

Résumé: 1. Elemental analysis of biological calcified structures (e.g. fish otoliths, mollusc shelves, coral skeletons or fish and shark bones) provides invaluable information regarding ecological processes for many aquatic species. Despite this importance, the reduction of the raw data obtained through Laser-ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICPMS) (i.e. the conversion of the machine raw signal into elemental concentrations) remains a challenge as the tools developed so far for carrying out this task have important limitations for aquatic ecologists. 2. Here, we introduce the elementr R-package which provides a handy, reliable and transparent way to reduce elemental data acquired from spot or transect LA-ICPMS analysis of biological calcified structures. This free and open-source software, implemented based on state-of-the-art literature, handles data from both standards and samples, allowing fast and simultaneous calculations of concentration for any chemical element, correction for potential machine drift, and realignment and averaging for sample replicates when needed. 3. The major attributes of elementr are: (i) its user-friendly graphical interface which provides widgets to set all the reduction settings (i.e. no programming skills are required to run it), (ii) its reactivity whereby the software continuously observes any setting change made by the user, re-calculates and displays all updated results, allowing therefore users to visually check the validity of their settings and to tune them if needed and (iii) an object oriented underlying that facilitates subsequent handling of LA-ICPMS data in R. 4. Despite the elementr design being most suited to the needs of aquatic ecologists, its use could be broadened to other research fields (i.e. geology, material engineering) due to its flexibility. Moreover, the open-source approach used for programming this software allows its expansion in order to refine calculation procedures or to add new functionalities.

Résumé: With the persistence of a drought since the late 1960s, some West African estuaries became permanently reversed in term of salinity gradient and hypersaline waters are present in their upstream part (salinity >60). To understand the mechanisms regulating fish recruitment intensity in these estuaries and evaluate the consequences of freshwater shortages on juvenile habitat quality, a growth study was conducted in the Saloum hypersaline estuary (Senegal). The Mugilidae fish family, highly representative of estuarine environments, was targeted and several species sampled (Chelon dumerili, Mugil bananensis and M. cf. curema sp. M). Juveniles were sampled monthly all the year round in three areas of the estuary exhibiting strongly contrasted habitat conditions. Otolith sections were used to estimate the ages, reconstruct growth trajectories, estimate the duration of the oceanic larval phase, and evaluate juvenile growth variability along the salinity gradient. Analyses revealed that the temporal recruitment variability of C. dumerili, with 2 annual cohorts, was not mainly induced by growth-selection mechanisms, but probably more by predation pressures. Juveniles exhibited significantly faster growth rates in the lower salinity suggesting that benthic food availability was a strong factor controlling habitat quality of early juveniles. Salinity had also a clear impact when reducing the growth in hypersaline conditions and/or selecting slower growing individuals. Moderate freshwater inputs positively affected the nursery function of the estuary for mugilids by enhancing the productivity of the first trophic levels. In a long term, the global change could have an impact of the mugilid fishery and its management.

Résumé: Besides their important contribution to global biodiversity, mangroves provide many services. Nevertheless, due to an increase of human activities and to climate change, in less than 20 years these ecosystems have lost one fifth of their global surface area. In response to this decrease, mangrove reforestation incentives have spread throughout the world. The scientific and societal legitimacy of reforestation actions still remain in question. Focusing on two case studies, the Saloum Delta and Lower Casamance, Senegal, our methodology was mainly based on the analysis of environmental narratives and discourses between 2009 and 2013, and on reforestation campaigns conducted by NGOs. We highlight the complexity of the system of values associated with the mangroves, as well as the positive and negative interactions between the services. Even although the reforestation campaigns were generally successful in terms of reforested surfaces and international visibility, they were poor in terms of biological and cultural diversities and led to spatial injustice. Moreover, the extensive reforestation with a unique mangrove species, Rhizophora mangle, was perceived as means of ‘green grabbing’, and the simultaneous buying of carbon tax by industrial conglomerates induced disempowerment of the local communities. More integrated research programmes must be developed towards the extensive knowledge of the mangroves.

Résumé: Age and growth of Rhizoprionodon acutus were estimated from vertebrae age bands. From December 2009 to November 2010, 423 R. acutus between 37 and 112 cm total length (LT) were sampled along the Senegalese coast. Marginal increment ratio was used to check annual band deposition. Three growth models were adjusted to the length at age and compared using Akaike's information criterion. The Gompertz growth model with estimated size at birth appeared to be the best and resulted in growth parameters of L∞ = 139·55 (LT) and K = 0·17 year−1 for females and L∞ = 126·52 (LT) and K = 0·18 year−1 for males. The largest female and male examined were 8 and 9 years old, but the majority was between 1 and 3 years old. Ages at maturity estimated were 5·8 and 4·8 years for females and males, respectively. These results suggest that R. acutus is a slow-growing species, which render the species particularly vulnerable to heavy fishery exploitation. The growth parameters estimated in this study are crucial for stock assessments and for demographic analyses to evaluate the sustainability of commercial harvests.

Résumé: This study describes some biological parameters including length-weight relationships and condition factors of Epinephelus aeneus (Geoffroy Saint Hilaire, 1817) in the western coasts of Senegal (Joal,

Résumé: The exceptional biodiversity and productivity of tropical coastal lagoons can only be preserved by identifying the causes for the decline in the populations living in these vulnerable ecosystems. The Terminos lagoon in Mexico provided an opportunity for studying this issue as some of its fish populations, in particular the Silver Perch (Bairdiella chrysoura), have declined significantly since the 1980s. Fish sampling campaigns carried out over the whole lagoon area in 1979–81 and again in 2006–2011 revealed the mechanisms which may have been responsible for this decline. Based on biometrical data for 295 juveniles and adults from the two periods and on somatic growth derived from 173 otoliths, a study of the temporal changes in the demographic structure and life history traits (individual growth and body condition) made it possible to distinguish the causes of the decline in the B. chrysoura population. Growth models for the lagoon in 1980–1981 and 2006–2011 showed no significant change in the growth parameters of the population over the last 30 years with a logistic model giving an accurate estimate (R2 = 0.66) of the size-at-age for both periods. The decline in the B. chrysoura population could not be explained by an overall decrease in individual size and condition in the lagoon, the average standard length (SL) and Fulton index (FI) having increased slightly since 1980–1981 (4.6 mm and 0.02 for juveniles and 5.42 mm and 0.07 for adults). However, the size structure of the population in the lagoon has changed, with a significant shift in the size distribution of juveniles with a marked reduction in the proportion of juveniles ≤ 60 mm in the captures (90.9% fewer than in 1980–1981). As the otolith growth rate of fish during the first 4 months also decreased significantly between the two sampling periods (−15%), it is suggested that the main reason for the decline in the abundance and biomass of B. chrysoura within this system may be that its habitats are less suitable for fish growth and survival in the initial months after settlement. Environmental conditions in the lagoon appear to allow compensatory growth of the individuals that survive this early demographic bottleneck. The key for the conservation of B. chrysoura probably lies in the identification and restoration of the habitats required by its larvae and juveniles.

Résumé: The black-chinned tilapia Sarotherodon melanotheron heudelotii Rüppell 1852 (Teleostei, Cichlidae) displays remarkable acclimation capacities. When exposed to drastic changes of salinity, which can be the case in its natural habitat, it develops quick physiological responses and keeps reproducing. The present study focused on the physiological impact of salinity on male reproductive capacities, using gene expression as a proxy of acclimation process. Two series of experimental fish were investigated: the first one was composed of fish maintained in freshwater for several generations and newly acclimated to salinities of 35 and 70, whereas the second one consisted of the descendants of the latter born and were raised under their native salinity. Expression patterns of 43 candidate genes previously identified from the testes of wild males was investigated in the three salinities and two generations. Twenty of them showed significant expression differences between salinities, and their predicted function revealed that most of them are involved in the osmotic tolerance of sperm cells and/or in the maintenance of sperm motility. A high level of expression variation was evidenced, especially for fish maintained in freshwater. In spite of this, gene expression patterns allowed the differentiation between fish raised in freshwater and those maintained in hypersaline water in both generations. Altogether, the results presented here suggest that this high variability of expression is likely to ensure the reproductive success of this species under varying salinities.

Résumé: In Senegal, a significant decrease in catches indicates that many demersal fish stocks are being overexploited. The white grouper Epinephelus aeneus, locally known as the 'thiof', is exploited by both small-scale and industrial fisheries. A 28-year database of E. aeneus catches along the Senegalese coast provided by the Centre for Oceanographic Research of Dakar-Thiaroye, and size at maturity measured in Dakar (Senegal) from monthly samples in 2010, were used to analyse changes in population structure in the area over the past 37 years. Catches from the northern fishing areas were lower than those from the southern fishing areas, and decreased steadily during the period (Kolmogorov-Smirnov test, D = 0.243, p = 0.0002). The individual mean weight of catches decreased from 1974 to 2010 (linear regression, r(2) = 0.40, n = 37) and only 60% of the individuals were mature. The calculated sizes at maturity were 49 cm total length (TL) for females and 55 cm for males, and the optimal length of capture for a sustainable fishery was 96 cm, but only 0.03% of E. aeneus caught reached this length. Most of the catch consisted of juveniles; the larger reproductive individuals had disappeared. The number of individuals caught decreased significantly between 1974 and 2010 (1974-1983, r(2) = 0.98, n = 74 674; 1984-1993, r(2) = 0.95, n = 96 696; 1994-2003, r(2) = 0.93, n = 12 619; 2004-2010, r(2) = 0.91, n = 12 887), whereas the length range remained the same (10-110 cm TL). Biological indicators clearly showed that E. aeneus stocks in Senegal are overexploited and the species is now endangered. Immediate active management of fishing pressure is needed, therefore, to maintain E. aeneus populations in the area. Our results suggest a minimum size of <50 cm should be introduced and that fishing effort should be reduced.