The status of the world's land and marine mammals: diversity, threat, and knowledge

Knowledge of mammalian diversity is still surprisingly disparate, both regionally and taxonomically. Here, we present a comprehensive assessment of the conservation status and distribution of the world's mammals. Data, compiled by 1700+ experts, cover all 5487 species, including marine mammals. Global macroecological patterns are very different for land and marine species but suggest common mechanisms driving diversity and endemism across systems. Compared with land species, threat levels are higher among marine mammals, driven by different processes (accidental mortality and pollution, rather than habitat loss), and are spatially distinct (peaking in northern oceans, rather than in Southeast Asia). Marine mammals are also disproportionately poorly known. These data are made freely available to support further scientific developments and conservation action

Caractérisation et quantification moléculaires de l’écosystème microbien d’altération du saumon cru et des crevettes cuites

Raw salmon and cooked shrimp sold in supermarket are usually found under vacuum or CO2 modified atmosphere packaging (MAP). This type of packaging inhibit growth of some bacteria, therefore, CO2 tolerant bacteria dominate spoilage microbiota of these products. The aim of this study is to improve knowledge about bacteria involved in spoilage. Spoilage microbial ecosystems of raw salmon and tropical cooked shrimp were described using classic miocrobiological and molecular methods like PCR-TTGE and pyrosequencing. Lactic acid bacteria, notably Lactococcus piscium, Carnobacterium maltaromaticum, Carnobacterium divergens, Lactobacillus sakei, and Gram negative bacteria like Photobacterium phosphoreum and Enterobacteriaceae (Serratia spp.) has been described as dominant bacterial groups on spoiled MAP salmon by using both type of methods. Shewanella baltica and C. maltaromaticum were mostly present in spoiled entire tropical cooked shrimp while, Carnobacterium spp., Leuconostoc spp. and Streptococcus parauberis dominated spoiled peeled tropical cooked shrimp analyzed with pyrosequencing. In order to identify the bacteria responsible for these products spoilage, spoilage potential of several of these species was investigated using sterile matrix inoculation. Then, combining sensory, chemical, microbiological and molecular methods, spoilage of the inoculated samples was characterized. Volatile compounds analysis (GC-MS) of some samples was also realized. C. maltaromaticum and S. baltica are both implied in entire tropical cooked shrimp spoilage and P. phosphoreum was revealed to be responsible for MAP salmon spoilage. As no specific medium is available for enumeration of P. phosphoreum species in seafood products, a real time PCR method combined with propidium monoazide treatement was , thus, developed and used to quantify viable cells of this bacteria in salmon samples.Le saumon frais et les crevettes cuites commercialisés dans la grande distribution sont souvent présentés sous forme de portions conditionnées sous vide ou sous atmosphère enrichie en CO2. Cette atmosphère protectrice inhibe la croissance de certaines bactéries, cependant, d’autres bactéries tolérantes au CO2 vont dominer le microbiote d’altération de ces produits. L’objectif de cette thèse a été d’approfondir la connaissance de la flore à l’origine de leur altération. La description de l’écosystème microbien d’altération des pavés de saumon et des crevettes tropicales cuites a été réalisée à l’aide de méthodes microbiologiques traditionnelles et moléculaires comme la PCR-TTGE et le pyroséquençage. Les bactéries lactiques, notamment Lactococcus piscium, Carnobacterium maltaromaticum, Carnobacterium divergens, Lactobacillus sakei ainsi que des bactéries à Gram négatif comme Photobacterium phosphoreum et des entérobactéries (Serratia spp.) ont été considérées comme groupes bactériens dominants au moment de l’altération du saumon cru sous atmosphère protectrice par ces deux types de méthodes. Shewanella baltica et C. maltaromaticum étaient les bactéries majoritairement présentes dans les crevettes tropicales cuites entières altérées alors que les bactéries lactiques comme Carnobacterium spp., Leuconostoc spp. et Streptococcus parauberis constituaient le groupe bactérien dominant des crevettes tropicales cuites décortiquées altérées analysées par pyroséquençage. Afin d’identifier les bactéries responsables de l’altération de ces produits, le potentiel d’altération de plusieurs de ces espèces a été étudié en réalisant des inoculations sur produits stériles. L’altération de ces échantillons a ensuite été caractérisée grâce à une combinaison de méthodes sensorielles, chimiques, microbiologiques et moléculaires. L’analyse des composés volatils par chromatographie en phase gazeuse couplée à la spectrométrie de masse (GC-MS) a également été réalisée pour certains échantillons. C. maltaromaticum et S. baltica sont toutes deux impliquées dans l’altération des crevettes tropicales entières cuites et P. phosphoreum s’est révélée être la bactérie responsable de l’altération du saumon cru sous atmosphère protectrice. Aucune méthode classique de quantification spécifique de P. phosphoreum n’étant disponible, une méthode de PCR en temps-réel combinée à un traitement préalable des échantillons au propidium monoazide (PMA) a ensuite été développée et appliquée avec succès, dans le but de dénombrer les cellules viables de cette bactérie dans des échantillons de saumon cru

Instabilité des berges de la Dordogne : analyse et propositions d'interventions : t.1 Département de la Dordogne : t.2 Département de la Gironde : t.3 Départements du Lot et de la Corrèze

EPIDOR has been made responsible for defining an intervention strategy to guarantee the coherent management of the banks at inter-departmental level, taking into account the priorities of local authorities. This document includes an analytical section common to all the departments which serves as a basis for developing a global strategy for taking these particular phenomena into account. It presents technical solutions and estimates the cost of carrying them out. Departmental documents complete the global analysis and show its application at local level. They propose intervention strategies by department at the level of the communes concerned.EPIDOR a été chargé de définir une stratégie d'intervention garantissant une gestion des berges cohérente au niveau interdépartemental et prenant en compte les priorités des collectivités. Ce document comporte une partie analytique commune à tous les départements qui sert de base à l'élaboration d'une stratégie globale de prise en compte de ces phénomènes particuliers. Elle présente des solutions techniques et en estime les coûts de réalisation. Des documents départementaux viennent compléter l'analyse globale et en traduisent l'application locale. Ils proposent par département des stratégies d'intervention au niveau des communes concernées

Genetic diversity analysis of isolates belonging to the Photobacterium phosphoreum species group collected from salmon products using AFLP fingerprinting

An accurate amplified fragment length polymorphism (AFLP) method, including three primer sets for the selective amplification step, was developed to display the phylogenetic position of Photobacterium isolates collected from salmon products. This method was efficient for discriminating the three species Photobacterium phosphoreum, Photobacterium iliopiscarium and Photobacterium kishitanii, until now indistinctly gathered in the Photobacterium phosphoreum species group known to be strongly responsible for seafood spoilage. The AFLP fingerprints enabled the isolates to be separated into two main clusters that, according to the type strains, were assigned to the two species P. phosphoreum and P. iliopiscarium. P. kishitanii was not found in the collection. The accuracy of the method was validated by using gyrB-gene sequencing and luxA-gene PCR amplification, which confirmed the species delineation. Most of the isolates of each species were clonally distinct and even those that were isolated from the same source showed some diversity. Moreover, this AFLP method may be an excellent tool for genotyping isolates in bacterial communities and for clarifying our knowledge of the role of the different members of the Photobacterium species group in seafood spoilage

Convention de recherche 2011-2014 ONF / Irstea Nogent-sur-Vernisson. Rapport de la tranche 2012-2013

Rapport sur la convention de recherche sur les forêts de plaine. Le rapport comprend les avancées sur : - La modélisation des peuplements mélangés Chêne + autres - La modélisation des mélanges sapin - épicéa - hêtre, et leur implémentation dans le module Melies - L'étude locale du mélange Chêne sessile - Pin sylvestr

Characterisation of the spoilage microbiota in raw salmon (Salmo salar) steaks stored under vacuum or modified atmosphere packaging combining conventional methods and PCR-TTGE

International audienceIn order to characterise the spoilage related to microbiota of raw salmon, a combination of culture-dependent and -independent methods, including PCR-TTGE, was used to analyse 3 raw salmon batches stored for 3 days at chilled temperature in modified atmosphere packaging (MAP) (50% CO2/50% N-2) or under vacuum. Sensory evaluation, microbiological enumeration and chemical analysis were performed after 3, 7 and 10 days of storage. At the onset of spoilage, 65 bacterial isolates were picked from the plates. Thus, 13 different genera or species were identified by phenotypic and molecular tests: Serratia spp., Photobacterium phosphoreum, Yersinia intermedia, Hafnia alvei, Buttiauxella gaviniae, Pseudomonas sp., Carnobacterium maltaromaticum, Carnobacterium divergens, Lactococcus piscium, Lactobacillus fuchuensis, Vagococcus carniphilus, Leuconostoc gasicomitatum and Brochothrix thermosphacta. The PCR-TTGE profiles and band identification enabled a shift of the dominant populations during the storage to be visualised for all the batches, probably due to the temperature change and the packaging. At the beginning of storage, Pseudomonas sp. dominated the raw salmon microbiota while in the following days (7 and 10), P. phosphoreum and L piscium were identified as the main bacterial groups. This study enhances the knowledge of MAP and vacuum-packed raw salmon spoilage microbiota. (C) 2011 Elsevier Ltd. All rights reserved

Occurrence and diversity of thermophilic sporeformers in French dairy powders

This study reports the prevalence of sporeforming bacteria and contamination levels of a variety of powdered dairy products from cows’, ewes’, goats’ and mares’ milk produced in France. The concentration of mesophilic spores, thermophilic spores and highly heat-resistant thermophilic spores was assessed in 61 dairy powders. Thermophilic spore concentration was highly variable between powders, likely due to the different manufacturing processes used for transforming milk into dairy powders. The different stages of processing, particularly heat treatment close to 55 °C had a strong impact on selection of thermophilic bacteria contaminating dairy powders. For some products, thermophilic spore counts were as high as 5.89 log TSC g-1. Of the 313 thermophilic isolates selected, 93.3% belonged to the species Geobacillus stearothermophilus (43.5%), Bacillus licheniformis (30.0%) and Anoxybacillus flavithermus (19.8%). These results confirm the presence of the three majority species reported worldwide

Evaluation of the spoilage potential of bacteria isolated from spoiled cooked whole tropical shrimp (Penaeus vannamei) stored under modified atmosphere packaging

The spoilage potential of isolates belonging to five bacterial groups/species (Shewanella baltica, Carnobacterium maltaromaticum, Aeromonas salmonicida, Vibrio sp., “other Gamma-Proteobacteria” [containing one strain of Pseudoalteromonas sp. and one strain of Psychrobacter sp.]) isolated from spoiled cooked and whole tropical shrimp stored under modified atmosphere packaging (MAP) was evaluated by inoculation into ionized cooked and peeled tropical shrimp followed by storage for 32 days at 8°C. Microbial growth and sensory changes were monitored during the storage period. The major spoilage bacterial isolate groups were C. maltaromaticum and S. baltica. In order to characterize their spoilage potential further and to study the effect of their interactions, each of these two specific spoilage organisms (SSO) and one mixed-culture, C. maltaromaticum/S. baltica, were tested using a combination of complementary methods: molecular (PCR-TTGE), sensory, chemical, and conventional microbiological analyses. It was concluded that, in the mixed-culture-inoculated samples, both species groups imposed their spoilage characteristics