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International audience; Free-range systems provide an outdoor range for broilers to give them the possibility to express a higher frequency and a wider range of behaviours, such as exploration, compared with those raised indoors. Greater variability in outdoor range use between individuals of the same flock is often reported. Individual variation in range use may result from differences in early-life behaviour or genetic background. Understanding how earlylife behaviour influences range use may provide opportunities to enhance and predict range use. Previous studies have shown that range use could be influenced by the animal’s personality traits such as social motivation, boldness and foraging motivation. Therefore, this study investigated personality traits in several broiler strains, namely Hubbard JA757, Hubbard S757N, White Bresse and a dual-purpose strain; we examined the latter as it represents a potential solution to the ban of 1-day-old chick culling. The present study also investigated early-life behaviours, before range access, of range use to identify and assess the stability of these early-life indicators among the four broiler strains. For that purpose, we recorded the behaviour and range use of 100 male chickens per strain, both in the barn and during individual tests, before and after range access. We examined which behaviours were time consistent, whether early-life behaviours were influenced by genetic variation and whether early-life behavioural indicators predicted range use regardless of genetic variation. There was a significant (p < 0.001) difference between strains in several early-life behaviours, including the time spent resting or standing. Range use was time consistent regardless of the strain as our range use indicator followed a high-quality linear regression model (R2 > 0.7) for 82–99% of the individuals depending on their strain. Besides, time consistency of social motivation and boldness seemed to depend on the strain. Even though foraging showed low (rho = 0.2–0.4) positive correlations with range use in three of the four studied strains, there were no significant and strong correlations in the four studied strains between early-life behavioural indicators and range use. In conclusion, our results show that the link between chick behaviour (before range access) and range use can be modulated by the bird’s strain. It is crucial to consider all these different factors to better understand how range use varies within and between flocks.

International audience

Chronic stress and the gut microbiota appear to comprise a feed-forward loop, which contributes to the development of depressive disorders. Evidence suggests that memory can also be impaired by either chronic stress or microbiota imbalance. However, it remains to be established whether these could be a part of an integrated loop model and be responsible for memory impairments. To shed light on this, we used a two-pronged approach in Japanese quail: first stress-induced alterations in gut microbiota were characterized, then we tested whether this altered microbiota could affect brain and memory function when transferred to a germ-free host. The cecal microbiota of chronically stressed quails was found to be significantly different from that of unstressed individuals with lower α and β diversities and increased Bacteroidetes abundance largely represented by the Alistipes genus, a well-known stress target in rodents and humans. The transfer of this altered microbiota into germ-free quails decreased their spatial and cue-based memory abilities as previously demonstrated in the stressed donors. The recipients also displayed increased anxiety-like behavior, reduced basal plasma corticosterone levels and differential gene expression in the brain. Furthermore, cecal microbiota transfer from a chronically stressed individual was sufficient to mimic the adverse impact of chronic stress on memory in recipient hosts and this action may be related to the Alistipes genus. Our results provide evidence of a feed-forward loop system linking the microbiota-gut-brain axis to stress and memory function and suggest that maintaining a healthy microbiota could help alleviate memory impairments linked to chronic stress. Availability of data and materials The datasets used during the current study are available from the corresponding author on reasonable request and they are available at https://doi.org/10.15454/JYITK4 .

Chronic stress and the gut microbiota appear to comprise a feed-forward loop, which contributes to the development of depressive disorders. Evidence suggests that memory can also be impaired by either chronic stress or microbiota imbalance. However, it remains to be established whether these could be a part of an integrated loop model and be responsible for memory impairments. To shed light on this, we used a two-pronged approach in Japanese quail: first stress-induced alterations in gut microbiota were characterized, then we tested whether this altered microbiota could affect brain and memory function when transferred to a germ-free host. The cecal microbiota of chronically stressed quails was found to be significantly different from that of unstressed individuals with lower α and β diversities and increased Bacteroidetes abundance largely represented by the Alistipes genus, a well-known stress target in rodents and humans. The transfer of this altered microbiota into germ-free quails decreased their spatial and cue-based memory abilities as previously demonstrated in the stressed donors. The recipients also displayed increased anxiety-like behavior, reduced basal plasma corticosterone levels and differential gene expression in the brain. Furthermore, cecal microbiota transfer from a chronically stressed individual was sufficient to mimic the adverse impact of chronic stress on memory in recipient hosts and this action may be related to the Alistipes genus. Our results provide evidence of a feed-forward loop system linking the microbiota-gut-brain axis to stress and memory function and suggest that maintaining a healthy microbiota could help alleviate memory impairments linked to chronic stress.

International audience; Animals can navigate an environment relying on different sources of information, such as geometrical or featural cues. The favoring of one type of information over another depends on multiple factors, such as inter-individual differences in behavior and cognition. Free-range chickens present different range use patterns, which may be explained by behavioral and cognitive differences. However, how behavior, cognition, and range use intercorrelate is still poorly understood. In this work, we aimed to further understand possible differences in behavior and cognition between two groups of free-range broiler chickens: those who frequently explore their range ('high rangers') and those who prefer to stay in or near the barn ('low rangers'). Prior to range access, individual behavior was measured in open field-, emergence-, and social motivation tests. To investigate cognitive differences, we analyzed whether exploratory behavior was linked to different performances in the use of distal and local spatial cues during an orientation task. During the social motivation test, low rangers showed a higher inclination to be near conspecifics than did high rangers. Our orientation tests show that chickens preferred to orientate themselves using the local cues over the distal cues. Individual differences were only found for distal, but not for local, cue use suggesting that demanding tasks are more efficient in revealing individual cognitive differences. Our results suggest that considering variation in social motivation may allow a more comprehensive understanding of chicken range use. Our results also support the importance of incorporating multiple aspects of individual differences to understand individual reactions to its environment.

International audience; Inhibiting impulsive, less flexible behaviours is of utmost importance for individual adaptation in an ever-changing environment. However, problem-solving tasks may be greatly impacted by individual differences in behaviour, since animals with distinct behavioural types perceive and interact with their environment differently, resulting in variable responses to the same stimuli. Here, we tested whether and how differences in ranging behaviour of free-range chickens affect motor self-regulation performance during a cylinder task. For this task, subjects must refrain from trying to reach a food reward through the walls of a transparent cylinder and detour to its open sides, as a sign of inhibition. Free-range chickens exhibited an overall low performance in the motor self-regulation task (31.33 +/- 13.55% of correct responses), however, high rangers showed significantly poorer performance than the low rangers (23.75 +/- 9.16% versus 40 +/- 12.90%, respectively). These results give further support to the impacts of individual behavioural differences on cognitive performances. This is the first demonstration to our knowledge of a relationship between exploratory tendencies and motor self-regulation for an avian species.

National audience; Mesurer précisément l'ingestion individuelle journalière des animaux est essentiel à de nombreuses questions de recherches. Le challenge est plus difficile à relever pour des animaux élevés en groupe, et plus encore s'ils sont élevés à l'extérieur (parcours, pâturage). L'objectif de ce travail est de faire le bilan des méthodes existantes, de les hiérarchiser en termes de précision, de conditions d'utilisation, de pertinence, de faisabilité, et ceci pour les principaux animaux de rente (bovins, ovins, caprins, équins, porcins, lapins, volailles). Les méthodes existantes ont été développées essentiellement pour les ruminants au pâturage, et depuis plus de 50 ans pour les plus anciennes. Elles se classent en deux grands types: les méthodes directes et les méthodes indirectes. Les méthodes directes sont basées sur des pesées: 1) pesée de l'animal entier avant et après une séquence d'ingestion, avec correction des pertes et prise en compte de la durée effective d'ingestion sur la séquence, 2) pesée d'une partie de l'animal (jabot des volailles, contenu du rumen des ruminants), ou 3) "pesée"du couvert végétal avant et après pâturage, par fauche mécanique. Cette dernière méthode ne permet que la mesure de l'ingestion du groupe, sauf si chaque animal n'a accès qu'à une zone de pâturage. Elle peut être relativement précise pour des couverts homogènes moyennant une forte pression de mesures, notamment post-pâturage. Les méthodes indirectes sont les plus fréquemment utilisées et peuvent être classées en trois sous groupes: 1) par estimation de l'excrétion fécale et de la digestibilité, 2) par l'utilisation combinée d'alcanes internes et externes, et 3} par mesure des composantes du comportement animal. Toutes les méthodes répertoriées sont chronophages, au champ, sur l'animal, et/ou au laboratoire. Seules les méthodes indirectes basées sur l'emploi de marqueurs externes permettent une mesure relativement précise de l'ingestion journalière individuelle (erreur moyenne à l'échelle individuelle de 1 0%). En expérimentation, elles permettent de détecter des écarts d'ingestion de 5 à 10% entre traitements selon la puissance du schéma expérimental, et peuvent donc être considérées comme les méthodes de référence. L'application de ces méthodes de référence, développées sur ruminants et équins, au cas des porcins, lapins et volailles élevés en extérieur peut comporter de sérieuses limites pratiques concernant à la fois la distribution quotidienne des marqueurs et l'échantillonnage individuel des fèces. Cela nécessite dans tous les cas des études de validation en milieu confiné avec contrôle de l'ingestion et variations du régime alimentaire pour étudier notamment la récupération fécale des marqueurs et si besoin la prévision de la digestibilité. Pour les animaux élevés en groupe en bâtiment, dont les aliments sont dans une mangeoire ou une auge, la pesée en continu de la mangeoire couplée à l'identification automatique, via des puces RFID, de l'animal ayant accès à la mangeoire constitue la méthode de référence. Pour être appliquée à tous types de filières, cette méthode nécessite cependant d'importants travaux de développement techniques pour adapter les dispositifs au format et au comportement alimentaire de l'espèce considérée, ainsi que des travaux spécifiques de développement informatique pour traiter les données de façon automatique. Des dispositifs commerciaux existent, mais ne permettent pas toujours l'accès aux données individuelles journalières. Par ailleurs, même s'ils permettent le contrôle des quantités ingérées, voire le rationnement des animaux, nombreux sont les dispositifs qui isolent l'animal mesuré de ses congénères dans un couloir durant le repas. Même si la hiérarchie entre animaux influe probablement l'accès à la mangeoire, les conditions de la mesure ne permettent donc pas totalement l'expression des comportements sociaux observés sur le terrain. Les nombreuses méthodes d'estimation de l'ingestion individuelle des animaux élevés en groupe, sont toutes chronophages, et les méthodes de référence les plus précises sont partiellement invasives du fait de l'administration à l'animal d'un marqueur. Elles ne peuvent être utilisées directement au pâturage sans études préalables de calibration, et toutes ne sont pas transposables aux animaux de petite taille pour d'évidentes raisons pratiques.

The interaction between the gut microbiota (GM) and the brain has led to the concept of the microbiota-gut-brain axis but data for birds remain scarce. We tested the hypothesis that colonization of germ-free chicks from a quail line selected for a high emotional reactivity (E+) with GM from a line with low emotional reactivity (E-) would reduce their emotional behaviour in comparison with germ-free chicks from an E+ line colonized with GM from the same E+ line. The GM composition analysis of both groups revealed a shift in terms of microbial diversity and richness between day 21 and day 35 and the GM of the two groups of quails were closer to each other at day 35 than at day 21 at a phylum level. Quails that received GM from the E- line expressed a lower emotional reactivity than quails colonized by GM from the E+ line in tonic immobility and novel environment tests carried out during the second week of age. This result was reversed in a second tonic immobility test and an open-field run 2 weeks later. These behavioural and GM modifications over time could be the consequence of the resilience of the GM to recover the equilibrium present in the E+ host, which is in part driven by the host genotype. This study shows for the first time that a GM transfer can influence emotional reactivity in Japanese quails, supporting the existence of a microbiota-gut-brain axis in this species of bird.

Different personalities may lead to different ways of processing environmental information; however, the relationship between personality and cognition is not fully understood as studies on diverse species present contrasting results. As there is great within-flock variability of outdoor ranging behavior in free-range broiler chickens, we tested whether and how ranging behavior impacts on individual spatial memory abilities. The experiment was conducted on one flock (n = 200) reared in the same conditions throughout the study, to simulate on-farm situations. As the ranging behavior was stable over time, we compared two distinct groups of male chickens: one that visited the range more (High rangers) and one that was more prone to staying in the poultry house (Low rangers). To test the spatial memory, individuals (n = 30) went through two main phases in an arena with 8 cups. For the familiarization phase, individuals were submitted to one trial per day, for seven days, to a situation where all eight cups were baited with mealworms. Animals had to reach a criterion of 5 cups visited out of 8 to advance to the next phase. For the spatial test, only four cups were baited and systematically placed at the same location. This last phase comprised two trials per individual per day, for nine days. During these two phases, latency to visit cups and the number of visits and revisits of all cups were recorded. Low ranger chickens took less time to attain the pre-established threshold of visiting 5 cups out of 8, over the familiarization phase. During the spatial test, the latency to visit four cups decreased between the within-day trials for low ranger chickens and increased for high ranger chickens. Moreover, in the within-day trial analysis, low ranger chickens exhibited an improvement on spatial memory and better spatial memory compared to high ranger chickens. Different speed-accuracy trade-offs may explain these differences between low and high ranger chickens and the way individuals interact and solve the task. Our study strengthens the scientific evidence relating consistent individual differences in behavior, with the ranging behavior of free-range chickens, and cognitive performance during a spatial memory task.

International audience; The interaction between the gut microbiota (GM) and the brain has led to the concept of the microbiota-gut-brain axis but data in birds remain scarce. We tested the hypothesis that colonization of germ-free chicks from a quail line selected for a high emotional reactivity (E+) with GM from a line with low emotional reactivity (E-) would reduce their emotional behaviour in comparison with germ-free chicks from E+ line colonized with GM from the same E+ line. The GM composition analysis of both groups revealed a shift in term of microbial diversity and richness between Day 21 and Day 35 and the GM of the two groups of quails were closer to each other at Day 35 than at Day 21 at a phylum level. Quails that received GM from the E- line expressed a lower emotional reactivity than the quails colonized by GM from the E+line in the tonic immobility and the novel environment tests proceeded during the second week of age. This result was reversed in a second tonic immobility test and an open-field run two weeks later. These behavioural and GM modifications over time could be the consequence of the resilience of the GM to recover its equilibrium present in the E+ host, which is in part driven by the host genotype. This study shows for the first time that a gut microbiota transfer can influence emotional reactivity in Japanese quails strengthening the existence of a microbiota-gut-brain axis in this species of bird.

International audience; Free-range broiler chickens usually show an uneven spatial utilization of an outdoor range. Due to behavioral and cognitive between-individual differences, some animals may be driven to associate food and conspecifics more strongly to the barn, causing them to be less prone to explore the range. In this study, we aimed to understand how broiler chickens with different ranging levels (low- and high-ranging chickens) would behave under conditioned place preference (CPP) test situations. We used two cohorts conditioned to two natural rewarding stimuli: food and social companions. In a two-chambered apparatus, one cohort (n = 31, 16 high-ranging, and 15 low-ranging chickens) was conditioned to one chamber that always contained a cup with a food reward (mealworms), while the cup in the other chamber was always empty. The same design was also used with the second cohort (n = 31, 15 high-ranging and 16 low-ranging chickens), although instead of food, the reward was the physical presence of two conspecifics. During the testing trials, the animals had access to both empty chambers, and the time spent in each chamber was quantified. For the first day of the food CPP test, both the high- and low-ranging chickens spent significantly more time in the conditioned chamber, where they had previously found mealworms. During the following extinction days, the animals showed a gradual loss of their learned preference, increasing their immobility in the apparatus. High-ranging chickens were more immobile than low-ranging chickens, however, as their number of trials without moving was significantly higher. Unexpectedly, during the first day of the social CPP test, only high-ranging chickens showed a place preference. An overall place preference was observed only on the second day, with no chamber preference during the extinction days. Our results suggest that whether and how a stimulus-reward association occurs for free-range chickens may also be dependent on individual differences and the nature of the reward (food or social). Since associative learning occurs on a daily basis for farmed animals and the way individuals learn or value the reward varies, this research advanced our knowledge of animal behavior and individual cognitive differences that can be highly beneficial in improving animals' living conditions; this new understanding will allow for a more individualized approach to rearing broiler chickens in outdoor systems.

The increasing cost of conventional feedstuffs used in poultry diets has bolstered interest in genetic selection for digestive efficiency (DE) to improve the adaptation of the birds to various alternative feedstuffs. However, DE measurement through AMEn is time-consuming and constraining. To simplify selection for DE, the potential of serum composition to predict AMEn was evaluated based on 40 birds from two broiler lines (D+ and D−) divergently selected on the fecal AMEn of a difficult-to-digest wheat-based diet. Differences in serum coloration were suspected between the two lines, and thus a spectrophotometric analysis was carried out, revealing a significant difference in absorption between 430 nm and 516 nm, corresponding to the signature of orange–red lipophilic pigments such as xanthophylls. To go further, the liposoluble fraction of the serum was explored for its lipidome by mass spectrometry. Discriminant analysis revealed that a pattern of 10 metabolites, including zeaxanthin/lutein, can explain 82% of the lipidomic differences between the two lines. Colorimetry combined with lipidomics studies confirmed the relationship between digestive efficiency and serum composition, which opens up new possibilities for using it as a quick and easy proxy of digestive efficiency.

International audience; In organic agricultural systems, swine and poultry must have access to roughage; in the case of rabbits, roughage must constitute 60% of the diet. Allowing access to forage could be a mechanism for reducing feed-related costs and the need to provide protein via complete feed. One issue is that the nutritional values of different forage types are poorly characterised for these monogastric species. However, based on available data, swine and poultry can at least partially exploit forage-based protein (digestibility: about 50% and 75%, respectively), even though they are not herbivorous. For rabbits, which are herbivorous, the nutritional value of forage is high. Different methods of allowing forage access could be used: turning animals out to grass or through feeding. However, several other issues must be explored before clear recommendations can be made to livestock farmers.; En agriculture biologique, les monogastriques doivent avoir accès à des fourrages grossiers (porcs et volailles) ou que ceux-ci représentent 60 % de leur alimentation (lapins). Les fourrages grossiers constituent une ressource locale disponible dans les systèmes d’élevage biologiques, qui présente un potentiel intéressant (bien que les porcs et les volailles ne soient pas herbivores) pour diminuer le coût alimentaire et le recours à des sources de protéines dans l’aliment complet. Leur valeur nutritionnelle est mal connue mais au vu des résultats disponibles, les porcs et les volailles sont en mesure d’en valoriser les protéines en partie (environ 50 % de digestibilité pour des porcs ; 75 % pour des volailles) alors que les apports énergétiques à attendre sont très faibles. Pour les lapins qui sont des herbivores monogastriques, leur valeur nutritionnelle est élevée. Différents modes de valorisation peuvent être envisagés : pâturage ou distribution à l'auge. En fonction des objectifs et du système d’élevage, une conduite de l’aliment complet avec rationnement et/ou appauvrissement de sa teneur en peut permettre, lorsqu’elle bien maîtrisée, permettre de maintenir des performances techniques élevées en diminuant le coût alimentaire. Cependant, de nombreuses pistes sont encore à explorer avant de proposer des recommandations consolidées aux éleveurs de monogastriques désirant valoriser au mieux les fourrages disponibles sur leur exploitation : niveaux de rationnement, formulation de l’aliment appauvrie en protéines, modalités de distribution, optimisation de la gestion du pâturage, choix des espèces végétales pour favoriser la consommation, en constituent quelques-unes.

La France est actuellement au premier rang des productions européennes de poulets et d’œufs biologiques. Ces productions ne représentent toutefois au mieux que quelques pourcents de la production nationale. Elles sont en régression pour le poulet ou stable pour l’œuf et ne couvrent pas les besoins du marché intérieur. Dans un contexte à la fois de demande du citoyen, d’une volonté politique nationale affichée et d’évolution du règlement européen, l’aviculture biologique française pourrait reprendre sa croissance en saisissant ces opportunités pour se développer. Aussi nous proposons d’analyser les atouts et les verrous qui caractérisent ce mode de production. Les analyses multicritères de ces productions restent à conduire à l’échelle du territoire. Elles devront prendre en compte les différentes composantes biotechniques, depuis la gestion agronomique des sols jusqu’au produit terminal, en passant par la production territorialisée des matières premières végétales, de même que les composantes économiques, sociétales ou politiques. Au-delà des images positives que les produits biologiques véhiculent en termes de bien-être, de qualité des produits ou de bilan environnemental, certaines contraintes déjà identifiées sont autant d’obstacles à leurs développements. Il convient donc de les analyser finement et de les prendre en compte afin de définir de nouveaux itinéraires de production et de ommercialisation. Ceux-ci devront permettre de concilier un développement cohérent et durable, répondant à des attentes sociétales complexes, de produire des produits de qualité, respectueux de l’environnement, accessibles au plus grand nombre et favorisant l’emploi rural et le développement des territoires. Cette problématique complexe constitue l’objet de deux programmes de recherches pluriannuels complémentaires initiés en 2009, AlterAviBio et AviBio., France currently leads European organic chicken and egg production. Each production, however, represents only a small percentage of national production. Organic production has declined for chicken and remains stable for eggs, but each does not cover the respective domestic demand. The French organic poultry industry could resume growth by taking advantage of new opportunities for development within a context that includes consumer pressures, expressed political will, and evolution of European regulations. We analyse the advantages and bottlenecks characteristic of these types of production. Multicriteria analyses of these production systems must be done at the national scale. They should include the various biotechnical components, from agricultural soil management to the final product, via regional production of raw vegetable matter, along with economic, social, and political components. Despite the positive image that organic products have in terms of animal welfare, product quality, or environmental respect, some previously identified constraints are obstacles to their development. It is therefore necessary to take them into account and carefully analyse them to define new production and commercial paths. These paths should accommodate a consistent and sustainable development, meet society's complex expectations, produce products of quality that respect the environment and are available to many, and favour rural employment and regional development. This complex problem is the object of two complementary pluriannual research programmes beginning in 2009, AlterAviBio and AviBio.

International audience; Free-range birds such as organic broilers may ingest soil and plants during exploration. The estimation of such intakes is of great interest to quantify possible nutritional supplies and also to evaluate the risk of exposure to parasites or to environmental contaminants. Marker-based techniques are now available and would allow to quantify plant and, especially, soil intake in freerange birds, and this quantification was the aim of this study. Methodologically, the proportion of plants in diet intake was determined first using a method based on n-alkanes. Subsequently, the fraction of soil in the total intake was estimated with a second marker, acid-insoluble ash. This approach was carried out to estimate ingested amounts of plants and soil for five successive flocks of organic broilers, exploring grass-covered yards or those under trees, at two time points for each yard: 51 and 64 days of age. Each factor combination (yard type x period = flock number x age) was repeated on two different yards of 750 broilers each. The birds' plant intake varied widely, especially on grass-covered yards. The proportion of plant intake was significantly higher on grass-covered plots than under trees and was also affected, but to a lesser extent, by age or flock number. The ingestion of plants would generally not exceed 11 g of DM daily, except two extreme outliers of nearly 30g. The daily plant intake under trees tended to be lower and never exceeded 7 g of DM. The amount of ingested plants increased significantly for spring flocks. It increased slightly but significantly with age. The proportion of ingested soil was significantly higher under trees than on grasscovered yards. Dry soil intake was generally low with not more than 3 g per day. Only in adverse conditions that is, older birds exploring yards under trees in winter soil intake reached the extreme value of nearly 5g. Broilers on yards under trees ingested significantly more soil than on grass-covered yards with least square means of, respectively, 2.1 and 1.1 g dry soil per day. These quantifications would allow us to evaluate the impact of plant and soil intake in the management of free-range broilers, especially for the management in organic farming systems. Nevertheless, under the two rearing conditions tested in the current study, the quite low proportions of soil intakes would represent a low risk for the safety of the produced food, unless the birds explore yards on heavily contaminated soil.

International audience; Two organic broilers rearing systems, each associated with a broiler house of 75 m2 and an outdoor run of 2500 m2, were studied. In the first system, the outdoor run consisted of grassland (GRASS) but in the second, the outdoor run was planted with oaks (TREE). Two batches of broilers were studied from winter to spring (WS) and from summer to autumn (SA). Indoor and outdoor airborne concentrations of NH3, N2O, CH4, CO2 and H2O weremeasured using a photoacoustic infrared analyser. Air flow rate through the broiler house was estimated using SF6 tracer gas. The final amount and composition of the manure was determined. A mass balance was determined for N, P and water. Results showed that in SA, more nutrients were excreted in the outdoor run (41%) compared with WS (11%). During the WS season, outdoor excretion was greater in the TREE system but this was notobserved during SA. Ammonia indoor emissions were higher during WS (200-283 mg [NH3] d-1 bird-1) than during SA (99-116 mg [NH3] d-1 bird-1). Total emissions from the systems (indoor þ outdoor) were assessed using our values and data from the literature for outdoor emissions. This confirmed that total NH3 emissions were in the same range as emissions of broilers reared in closed houses. N2O emissions were higher during WS but represented less than 0.5% of indoor N excretion. Total CH4 emissions were very low (40-60 mg [CH4] d-1 bird-1), particularly in comparison with emissions in other species.

absent

Small ruminants lentiviruses (SRLV) nucleotide sequences spanning the V1V2 variable regions of the env gene were amplified by nested-PCR from 38 blood samples collected from 16 naturally infected sheep flocks in France. For the rapid SRLV group determination of field isolates, the PCR-amplified fragments were subjected to a SRLV-adapted heteroduplex mobility assay (HMA). All viral sequences were clearly assignable to the SRLV group B by HMA analysis. Twenty-seven SRLV isolates were selected for DNA sequence analysis. In each case, nucleotide comparison and phylogenetic analyses confirmed the genetic relationships inferred by HMA. Six SRLV isolates belonged to subtype B1, and 21 pertained to subtype B2, one flock being infected with both subtypes. Subtypes B1 and B2 were found with different frequencies and geographic spread, but exhibited similar genetic diversities. These results give a more complete picture of the distribution and heterogeneity of SRLV env subtypes in sheep and confirmed that multiple interspecies transmission occurred in the past. Furthermore, HMA appeared to be a rapid and reliable method to differentiate caprine arthritis encephalitis virus from maedi-visna virus.

Summary Escherichia coli DNA polymerase III (Pol III) is one of the best studied replicative DNA polymerases. Here we report the properties of an E. coli mutant that lacks one of the subunits of the Pol III clamp loader complex, Psi (ψ), as a result of the complete inactivation of the holD gene. We show that, in this mutant, chronic induction of the SOS response in a RecFOR-dependent way leads to lethality at high temperature. The SOS-induced proteins that are lethal in the holD mutant are the specialized DNA polymerases Pol II and Pol IV, combined with the division inhibitor SfiA. Prevention of SOS induction or inactivation of Pol II, Pol IV and SfiA encoding genes allows growth of the holD mutant, although at a reduced rate compared to a wild-type cell. In contrast, the SOS-induced Pol V DNA polymerase does not participate to the lethality of the holD mutant. We conclude that: (i) Psi is essential for efficient replication of the E. coli chromosome; (ii) SOS-induction of specialized DNA polymerases can be lethal in cells in which the replicative polymerase is defective, and (iii) specialized DNA polymerases differ in respect to their access to inactivated replication forks.

International audience; Soil ingestion is recognized as the main source of environmental contaminants in food-producing animals reared outdoors. Therefore, its consumption should be quantified for proper risk assessment under practical circumstances. A quantitative method, involving the determination of acid-insoluble ash (AIA) in feces, was previously evaluated in several animal species. Nevertheless, this method is highly sensitive to feed digestibility, which may be influenced by the unknown amount of soil actually consumed. Besides, animals may ingest plants in addition to soil. Therefore the amount and the digestibility of plants ingested should also be known. The purpose of the current study was to assess a method for determining soil and plants ingested by free range chickens using AIA and odd-numbered n-alkanes (C25 to C31) as markers of soil and of plants, respectively. Ninety slow-growing chickens aged 38 days were placed in individual cages and given nine pelleted diets containing, in addition to standard feed, graded levels of soil and plants alone, or in combination (0 to 30% and 0 to 15% of diet dry matter (DM), respectively). After a 5-day adaptation period, excreta from each bird were collected in their entirety for three days. The energy retention coefficient (ERC) of feed alone and of plants was estimated to be 0.70 and 0.14, respectively. The presence of soil linearly depressed feed ERC but did not influence plant ERC. The effect of soil on feed ERC was quite low, reaching 0.02 for 30% of soil incorporation in diet DM. The average recovery rate of ingested n-alkanes in excreta was low (43%) and variable between n-alkanes and between diets, while AIA was totally recovered in all diets except in feed alone. After the concentration of each n-alkane in excreta was corrected by its mean recovery rate, comparison of the feed, plant and excreta profiles elicited an estimate of plant contribution to DM ingested biased by 0 to 2% of plant contribution to DM. Despite these biases and the slight influence of soil on feed ERC, introducing the ERC of feed alone into the soil-ingestion equation provided a good estimate of soil contribution to DM ingested. The sequential current methodology is a promising tool for evaluating soil ingestion by broilers reared outdoors under practical circumstances. However, further work is required to alleviate uncertainties concerning the impact of different types of soil on the ERC of feed given to animals.

Nitrous oxide (N2O), methane (CH4) and carbon dioxide (CO2) fluxes over the grassy outdoor run of organically grown broilers were monitored using static chambers over two production batches in contrasted seasons. Measured N2O and CH4 fluxes were extremely variable in time and space for both batches, with fluxes ranging from a small uptake by soil to large emissions peaks, the latter of which always occurred in the chambers located closest to the broiler house. In general, fluxes decreased with increasing distance to the broiler house, demonstrating that the foraging of broilers and the amount of excreted nutrients (carbon, nitrogen) largely control the spatial variability of emissions. Spatial integration by kriging methods was carried out to provide representative fluxes on the outdoor run for each measurement day. Mechanistic relationships between plot-scale estimates and environmental conditions (soil temperature and water content) were calibrated in order to fill gaps between measurement days. Flux integration over the year 2010 showed that around 3 ± 1 kg N2O-N ha−1 were emitted on the outdoor run, equivalent to 0.9% of outdoor N excretion and substantially lower than the IPCC default emission factor of 2%. By contrast, the outdoor run was found to be a net CH4 sink of about −0.56 kg CH4-C ha−1, though this sink compensated less than 1.5% (in CO2 equivalents) of N2O emissions. The net greenhouse gas (GHG) budget of the outdoor run is explored, based on measured GHG fluxes and short-term (1.5 yr) variations in soil organic carbon.

This study presents an assessment of gaseous emissions from an organic broiler production system composed of a broiler house and an outdoor run located on an INRA experimental farm. In the house, concentrations of NH3, N2O, CH4, CO2 and H2O were monitored during 56 days over 3 discontinuous periods. To assess gaseous emissions, both indoor and outdoor gas concentrations were monitored using a photo-acoustic infrared analyser. Air flow rates were estimated using SF6 tracer gas. Mass balances were also performed with zootechnical data to validate the measurements and interpolate data between measurement periods. Outdoor emissions of N2O and CH4 were measured using manual static chambers placed on the outdoor run. In the house, emissions were 0.13 g NH3 day-1 broiler-1, 46 mg N2O day-1 broiler-1 and 13 mg CH4 day-1 broiler-1. Indoor NH3 emissions were lower than for broilers raised in confinement, which can be explained because of the access to the outdoor run. Moreover, results showed that indoor gaseous N losses were 30 40% of total N excretion, which is consistent with the French inventory methodology. On the outdoor run, emissions of N2O and CH4 were low and close to background fluxes (< 40 ng s-1 m-2). Emission peaks were occasionally measured, especially in chambers close to the house where the density of droppings was higher. Finally, results showed that with good assessment of dropping distribution on the outdoor run, emissions of CH4 and N2O could be extrapolated over the whole rearing period at the outdoor run scale., Cette étude propose une estimation des émissions gazeuses à partir de mesures réalisées dans un élevage biologique sur le domaine INRA du Magneraud (17). Les émissions de NH3, N2O, CH4, CO2, et H2O du bâtiment ont été mesurées pendant 56 jours réparties sur 3 périodes de mesure. Pour ce faire les débits d'air ont été estimés au moyen d'un gaz traceur (SF6) et les concentrations ambiantes intérieures et extérieures en gaz mesurées à l'aide d'un analyseur de gaz infrarouge photo-acoustique. Des bilans de masse calculés à partir de données d'élevage ont également été réalisés pour valider les émissions mesurées et les interpolations sur toute la période d'élevage. Les émissions de N2O et de CH4 sur le parcours ont été mesurées au moyen de chambres statiques disposées sur le parcours. En bâtiment, les émissions gazeuses s'élevaient à 0,13 g NH3 jour-1 animal-1, 46 mg N2O jour-1 animal-1 et 13 mg CH4 jour-1 animal-1. Les émissions de NH3 en bâtiment sont plus faibles que pour des poulets élevés en claustration. Ceci peut s'expliquer par une excrétion azotée plus faible en bâtiment en raison de l'accès au parcours. Le bilan de masse sur l'azote a permis d'estimer les pertes totales azotées gazeuses entre 30 et 40% de l'excrété total, ce qui est en accord avec les données du CORPEN. Sur parcours, les émissions de N2O et de CH4 sont très faibles et proches des conditions de fond mesurées à l'extérieur du parcours (< 40 ng s-1 m-2). Toutefois, des pics d'émissions ont été observés aux abords du bâtiment, zone occupée préférentiellement par les animaux et avec une concentration élevée des déjections. Les résultats montrent qu'en estimant la répartition des déjections sur l'ensemble du parcours, les émissions totales à l'échelle du parcours et sur toute la période d'élevage pourront être estimées.

Organic chicken production facilities must provide an access to open air areas (outdoor runs) as specified in European Council Regulations. Yet, very few data on pollutant gas emissions by organic poultry production are available, especially concerning the outdoor runs. To assess trace gas emissions (NH3, N2O, CH4) from an organic broiler housing, gas concentrations were monitored using a photo-acoustic infrared analyser. Air flow rates were estimated using SF6 tracer gas. Concerning the outdoor run, N2O and CH4 emissions were measured using manual static chambers placed on the grassland. Concerning the housing, cumulated emissions of N-NH3 were 0.22, 1.72 and 4.01 g of N per broiler respectively for each measurement period. N-N2O emissions represented 1.09, 0.09 and 0.08 g of N per broiler respectively. CH4 emissions were very low and represented 0.01, 0.33 and 0.34 g of CH4 per broiler, respectively. On the outdoor-runs, emissions of N2O and CH4 were very low although peaks of emission were measured, especially on chambers close to the housing where faeces excretion is higher. Mass balances for N, P, K, Cu and Zn at the system level will be carried out in order to validate these results.

Small-ruminant lentiviruses (SRLVs) display a high genetic diversity and are currently classified into five genotypes and an increasing number of subtypes. The co-circulation of subtypes in restricted geographical regions, combined with the occurrence of cross-species infection, suggests the need for development of a large-scale screening methodology for rapid monitoring of the prevalence of the various genetic subtypes and their genetic evolution. Here, a heteroduplex mobility assay (HMA) was developed for the rapid identification of group B subtypes. The assay was validated for both the p14 nucleocapsid-coding region of the gag gene and the V1–V2 region of the env gene using a panel of reference standards and was applied to the genetic subtyping of SRLV field isolates from five mixed flocks in France. Subtyping of 75 blood samples using the env HMA revealed a preferential distribution of subtypes B1 and B2 in sheep and goats, despite direct evidence for interspecies transmission of both subtypes. Adding the gag HMA to the env HMA provided evidence for dual infection and putative recombination between subtypes B1 and B2 in five goats, and between groups A and B in one sheep. Phylogenetic analysis revealed that 100 % (23/23) and 96.7 % (30/31) of samples were correctly classified using the gag and env HMAs, respectively. These results indicate that dual infection and recombination may be a significant source of new variation in SRLV and provide a useful tool for the rapid genetic subtyping of SRLV isolates, which could be relevant for the development of more accurate diagnosis of prevalent SRLV strains in different countries.

This paper presents the greenhouse gas (GHG) budget of an organic broiler production system in France, composed of a broiler house and an outdoor run. The study was conducted over 1 year on an experimental farm. In the broiler house, emissions of N2O and CH4 were measured using photo-acoustic infrared spectrometryand air flow rates were estimated using SF6 as tracer gas. On the outdoor run, N2O and CH4 fluxes were measured using static chambers. Spatial and temporal gap-filling methods were used to provide annual estimates of emissions. In the broiler house, CH4 and N2O annual emissions from manure represented about 49 and 71 g CO2-equivalents (CO2-eq.)/kg live weight (LW), while non-biotic CO2 emissions (heating) represented about 68 g CO2-eq./kg LW, suggesting that manure accounted for about 65% of total indoor CO2-eq. emissions. On the outdoor run, N2O emissions were estimated to 86 g CO2-eq./kg LW, while CH4 emissions were found negligible (-1 g CO2-eq./kg LW). However, long-term C sequestration on the outdoor run should be investigated since measured short-term variations in soil organic carbon suggested that the run could display a sink activity and thus compensate for a portion of GHG emissions.

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This study presents an assessment of gaseous emissions from an organic broiler production system composed of a broiler house and an outdoor run. In the house, concentrations of NH3, N2O, CH4, CO2 and H2O were monitored during 56 days over 3 discontinuous periods. To assess gaseous emissions, both indoor and outdoor gas concentrations were monitored using a photo-acoustic infrared analyser (INNOVA 1312). Air flow rates were estimated using SF6 tracer gas. Mass balances were also performed with zootechnical data to validate themeasurements and interpolate data between measurement periods. Outdoor N2O and CH4 emissions were measured using manual static chambers placed on the outdoor run. In the house, emissions were 130 mg NH3 day-1 broiler-1, 46 mg N2O day-1 broiler-1 and 13 mg CH4 day-1 broiler-1 . Indoor NH3 emissions were lower than for broilers raised in confinement, which can be explained by the access to the outdoor run. On the outdoor run, emissions of N2O and CH4 were low and close to background fluxes (< 40 ng s-1 m-2). Emission peaks wereoccasionally detected, especially in chambers close to the house where the density of droppings was higher. With good assessment of dropping distribution on the outdoor run, emissions of CH4 and N2O could be extrapolated over the whole rearing period at the outdoor run scale