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Endozoicomonas bacteria are generally beneficial symbionts of diverse marine invertebrates including reef-building corals, sponges, sea squirts, sea slugs, molluscs, and Bryozoans. In contrast, the recently reported Ca. Endozoicomonas cretensis was identified as a vertebrate pathogen, causing epitheliocystis in fish larvae resulting in massive mortality. Here, we described the Ca. E. cretensis draft genome, currently undergoing genome decay as evidenced by massive insertion sequence (IS element) expansion and pseudogene formation. Many of the insertion sequences are also predicted to carry outward-directed promoters, implying that they may be able to modulate the expression of neighbouring coding sequences (CDSs). Comparative genomic analysis has revealed many Ca. E. cretensis-specific CDSs, phage integration and novel gene families. Potential virulence related CDSs and machineries were identified in the genome, including secretion systems and related effector proteins, and systems related to biofilm formation and directed cell movement. Mucin degradation would be of importance to a fish pathogen, and many candidate CDSs associated with this pathway have been identified. The genome may reflect a bacterium in the process of changing niche from symbiont to pathogen, through expansion of virulence genes and some loss of metabolic capacity. Genome Biology and Evolution, 10 (6) ISSN:1759-6653

Ecological intensification is a new concept in agriculture that addresses the double challenge of maintaining a level of production sufficient to support needs of human populations and respecting the environment in order to conserve the natural world and human quality of life. This article adapts this concept to fish farming using agroecological principles and the ecosystem services framework. The method was developed from the study of published literature and applications at four study sites chosen for their differences in production intensity: polyculture ponds in France, integrated pig and pond polyculture in Brazil, the culture of striped catfish in Indonesia and a recirculating salmon aquaculture system in France. The study of stakeholders' perceptions of ecosystem services combined with environmental assessment through Life Cycle Assessment and Emergy accounting allowed development of an assessment tool that was used as a basis for co-building evolution scenarios. From this experience, ecological intensifica-tion of aquaculture was defined as the use of ecological processes and functions to increase productivity, strengthen ecosystem services and decrease disservices. It is based on aquaecosystem and biodiversity management and the use of local and traditional knowledge. Expected consequences for farming systems consist of greater autonomy, efficiency and better integration into their surrounding territories. Ecological intensification requires territorial governance and helps improve it from a sustainable development perspective. International audience

Abstract. The last glacial period (LGP; ca. 110–10 kyr BP) was marked by the existence of two types of abrupt climatic changes, Dansgaard–Oeschger (DO) and Heinrich (H) events. Although the mechanisms behind these are not fully understood, it is generally accepted that the presence of ice sheets played an important role in their occurrence. While an important effort has been made to investigate the dynamics and evolution of the Laurentide ice sheet (LIS) during this period, the Eurasian ice sheet (EIS) has not received much attention, in particular from a modeling perspective. However, meltwater discharge from this and other ice sheets surrounding the Nordic seas is often implied as a potential cause of ocean instabilities that lead to glacial abrupt climate changes. Thus, a better comprehension of the evolution of the EIS during the LGP is important to understand its role in glacial abrupt climate changes. Here we investigate the response of the EIS to millennial-scale climate variability during the LGP. We use a hybrid, three-dimensional, thermomechanical ice-sheet model that includes ice shelves and ice streams. The model is forced off-line via a novel perturbative approach that, as opposed to conventional methods, clearly differentiates between the spatial patterns of millennial-scale and orbital-scale climate variability. Thus, it provides a more realistic treatment of the forcing at millennial timescales. The effect of both atmospheric and oceanic variations are included. Our results show that the EIS responds with enhanced ice discharge in phase with interstadial warming in the North Atlantic when forced with surface ocean temperatures. Conversely, when subsurface ocean temperatures are used, enhanced ice discharge occurs both during stadials and at the beginning of the interstadials. Separating the atmospheric and oceanic effects demonstrates the major role of the ocean in controlling the dynamics of the EIS on millennial timescales. While the atmospheric forcing alone is only able to produce modest iceberg discharges, warming of the ocean leads to higher rates of iceberg discharges as a result of relatively strong basal melting at the margins of the ice sheet. Our results clearly show the capability of the EIS to react to glacial abrupt climate changes, and highlight the need for stronger constraints on the ice sheet's glacial dynamics and climate–ocean interactions.

Simple Summary Using combinations of plant protein concentrates and EAA supplementation, high levels of replacement (50–75% of fishmeal protein) have been achieved in gilthead sea bream without affecting the growth performance or quality traits. It was confirmed in this study that 16% replacement of marine protein with plant protein meets the amino acid needs of sea bream. The results of the present study suggest the need to further investigate tissue-specific and species-specific responses in the timing and ability to regulate metabolism due to dietary nutrient utilization. Abstract Following a meal, a series of physiological changes occurs in fish as they digest, absorb and assimilate ingested nutrients. This study aims to assess post-prandial free amino acid (FAA) activity in gilthead sea bream consuming a partial marine protein (fishmeal) replacement. Sea bream were fed diets where 16 and 27% of the fishmeal protein was replaced by plant protein. The essential amino acid (EAA) composition of the white muscle, liver and gut of sea bream was strongly correlated with the EAA composition of the 16% protein replacement diet compared to the 27% protein replacement diet. The mean FAA concentration in the white muscle and liver changed at 4 to 8 h after a meal and was not different to pre-feeding (0 h) and at 24 h after feeding. It was confirmed in this study that 16% replacement of marine protein with plant protein meets the amino acid needs of sea bream. Overall, the present study contributes towards understanding post-prandial amino acid profiles during uptake, tissue assimilation and immediate metabolic processing of amino acids in sea bream consuming a partial marine protein replacement. This study suggests the need to further investigate the magnitude of the post-prandial tissue-specific amino acid activity in relation to species-specific abilities to regulate metabolism due to dietary nutrient utilization.

The effect of filleting on the microbiological, chemical and sensory properties of aquacultured sea bass (Dicentrarchus labrax) stored in ice was studied. Pseudomonads, H(2)S-producing bacteria (including Shewanella putrefaciens) and Brochothrix thermosphacta were the dominant bacteria at the end of the 16 day storage period in ice for both whole ungutted and filleted sea bass. Enterobacteriaceae were also found in the spoilage microflora of whole ungutted and filleted sea bass, but their counts were always lower than those of pseudomonads, H(2)S-producing bacteria (including S putrefaciens) and B thermosphacta. Total viable counts for whole ungutted sea bass were always lower than those for filleted sea bass samples. Of the chemical indicators of spoilage, TMA (trimethylamine) values of whole ungutted sea bass increased very slowly, whereas significantly higher values were obtained for filleted samples, with respective values of 0.253 and 1.515 mg N per 100 g muscle being reached at the end of their shelf-life (days 13 and 9 respectively). TVB-N (total volatile basic nitrogen) values showed a slight increase for whole ungutted sea bass during storage, reaching a value of 26.77 mg N per 100 g muscle (day 13), whereas for filleted fish a corresponding value of 26.88 mg N per 100 g muscle was recorded (day 9). TBA (thiobarbituric acid) values increased slowly for whole ungutted and filleted sea bass samples throughout the entire storage period, reaching final values of 4.48 (day 13) and 13.84 (day 9) mg malonaldehyde kg(-1) respectively. Sensory assessment of raw fish using the EC freshness scale gave a grade E for up to 5 days for whole ungutted sea bass, a grade A for a further 4 days and a grade B for an additional 4 days, after which sea bass was graded as C (unfit). Overall acceptability scores for odour, taste and texture of cooked whole ungutted and filleted sea bass decreased with increasing time of storage. The results of this study indicate that the shelf-fife of sea bass stored in ice, as determined by overall acceptability sensory scores and microbiological data, is 8-9 days for filleted and 12-13 days for whole ungutted fish. (C) 2003 Society of Chemical Industry. Journal of the Science of Food and Agriculture

We compare several statistical routines that may be used to calculate delta O-18 and SSS from paired coral Sr/Ca and delta O-18 measurements. Typically, the delta O-18(coral)-SST relationship is estimated by linear regression of coral delta O-18 vs. SST. If this method is applied, evidence should be given that at a particular site SST and SSS do not co-vary. In the tropical oceans, SST and delta O-18(sw) (SSS) often co-vary, and this will bias the estimate of the regression slope of delta O-18(coral)-SST. Using a stochastic model, we show that covariance leads to a bias in the coefficients of the univariate regression equations. As the slope of the delta O-18(coral)-SST relationship has known, we propose to insert this value for gamma(1) in the regression models. This requires that the constants of the regression equations are removed. To omit the constants, we propose to center the regression equations (i.e., to remove the mean values from the variables). The statistical error propagation is calculated to assess our ability to resolve past variations in delta O-18(sw) (SSS). At Tahiti, we find that the combined analytical uncertainties of coral delta O-18 and Sr/Ca equal the amplitude of the seasonal cycle of delta O-18(sw) (SSS). Therefore, we cannot resolve the seasonal cycle of SSS at Tahiti. At Timor, the error of reconstructed delta O-18(sw) (SSS) is lower than the magnitude of seasonal variations of delta O-18(sw) (SSS), and the seasonal cycle of delta O-18(sw) (SSS) can be resolved. (c) 2008 Elsevier Ltd. All rights reserved.

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