Grain legume-cereal intercropping enhances the use of soil-derived and biologically fixed nitrogen in temperate agroecosystems: a meta-analysis

Grain legumes are known for their benefits to deliver ecosystem services on provisioning of protein-rich food and feed, reducing greenhouse gas emissions through the symbiotic nitrogen fixation function and diversification of cropping systems. Intercropping is an agroecological practice in which two or more crop species are grown simultaneously in the same field, thereby maximizing the use of resources to enhance yields in low input systemsand the resilience of cropping systems. We quantified the effect of grain legume-cereal intercropping on the useof N resources in temperate agroecosystems, focusing on dinitrogen (N2) fixation and soil-derived nitrogenacquisition using a meta-analysis of 29 field-scale studies. We estimated and compared effects of different intercrop compositions (proportion of each species in the intercrops), fertilization rates, crop species, soil properties, and other management practices on the symbiotic N2 fixation and the acquisition of soil-derived nitrogenby the cereals and grain legumes. The proportion of N derived from N2 fixation was on average 14 % (95 % CI =[11, 16]) higher in intercropped grain legumes (76 %) compared to legume sole crops (66 %). On the other hand,intercropping reduced the amount of N2 fixed (kg ha−1) by about 15 %, when N2 fixation in inter- and solecropped legumes was expressed at equivalent density by compensating for the sown legume proportion in intercrops relative to their sole crop sowing rate. The results were mainly influenced by the intercrop composition,legumes species and the method used to quantify N2 fixation. Soil-derived nitrogen acquisition in intercroppedgrain legumes was significantly reduced (−47 %, 95 % CI = [−56, −36]) compared to sole crop legumes,expressed at equivalent density, while the soil N acquired by intercropped cereals was much higher (+61 %, 95% CI = [24, 108]) than in sole crop cereals. Total soil N acquisition (legume + cereal) was significantly higherin intercrops than in legume sole crops (+25 %, 95 % CI = [1, 54]), while there was no significant differencebetween intercrops and cereal sole crops. The meta-analysis confirms and highlights that intercropping consistently stimulates complementary N use between legumes and cereals by increasing N2 fixation by grain legumes and increasing soil N acquisition in cereals. Based on the results of this analysis it would be suggested thatcropping systems diversification via intercropping can be used for simultaneous production of both cereals andgrain legumes, while increasing the use of N-sources and reducing external inputs of N fertilizers, thereby enhancing the sustainability of agriculture

Maternal health and the placental microbiome

Over the past decade, the role of the microbiome in regulating metabolism, immune function and behavior in humans has become apparent. It has become clear that the placenta is not a sterile organ, but rather has its own endogenous microbiome. The composition of the placental microbiome is distinct from that of the vagina and has been reported to resemble the oral microbiome. Compared to the gut microbiome, the placental microbiome exhibits limited microbial diversity. This review will focus on the current understanding of the placental microbiota in normal healthy pregnancy and also in disease states including preterm birth, chorioamnionitis and maternal conditions such as obesity, gestational diabetes mellitus and preeclampsia. Factors known to alter the composition of the placental microbiota will be discussed in the final part of this review

Co-conception et évaluation de scénarios agronomiques de réintroduction de légumineuses dans un territoire de Bourgogne

Ce numéro est constitué d’articles issus de la seconde édition des Rencontres Francophones sur les Légumineuses (RFL2) qui s’est tenu à Toulouse (France) les 17 et 18 octobre 2018.Legume crops can help facing current environmental and food challenges, even if their areas havedecreased since several decades. The aims of our study were (i) to design with local stakeholdersagronomic scenarios of reintroduction of legumes into a French territory, (ii) to assess these scenariosex ante, and (iii) to discuss with the stakeholders the interest and conditions of their adoption in theterritory. The stakeholders involved were agricultural stakeholders (farmers, technical advisors),stakeholders from environmental organizations (water union, national park) and researchersThe first step was the description and assessment of current and alternative crop management plans,from national statistical data and face-to-face surveys. In a second step, the current territory (cropdistribution in the territory and cropping strategies) was described with local stakeholders, and was usedas a reference. In a third step, stakeholders discussed various sets of objectives and constraints relatedto their territory. Among eight scenarios proposed by stakeholders, four scenarios were simulated withthe tool used in the Coclick’eau approach. For each scenario, this tool optimizes an alternativedistribution of crops and cropping strategies, and assesses the agronomic, socio-economic andenvironmental performances. Finally, the results were discussed with stakeholders.Les légumineuses peuvent contribuer à relever les défis environnementaux et alimentaires actuels,mais leurs surfaces cultivées ont largement diminué. Les objectifs de notre étude étaient (i) deconcevoir, avec les acteurs locaux du Plateau Langrois (Bourgogne), des scénarios agronomiques deréintroduction de légumineuses, (ii) d'évaluer ex ante ces scénarios, et (iii) de discuter les conditions deleur mise en œuvre sur ce territoire. Les acteurs ayant participé étaient issus du monde agricole(agriculteurs, conseillers techniques), de l’environnement (syndicat d’eau, Parc National) et de larecherche.La première étape a consisté à décrire et évaluer les itinéraires techniques actuels et prospectifs à partirde données statistiques et de résultats d’enquêtes individuelles. Dans un second temps unereprésentation du territoire actuel (assolement de cultures et de façons de cultiver) a été construite avecles acteurs et nous a servi de point de référence. Les acteurs ont ensuite exprimé leurs attendus pource territoire. Parmi les huit pistes de scénarios ayant émergé, quatre ont fait l’objet d’une simulationavec l'outil Coclick'eau, qui optimise, pour chacun de ces scénarios, un assolement alternatif et calculeses performances agronomiques, socio-économiques et environnementales. Finalement, ces résultatsont été présentés et discutés avec les acteurs

Linkage to chromosome 2q32.2-q33.3 in familial serrated neoplasia (Jass syndrome)

Causative genetic variants have to date been identified for only a small proportion of familial colorectal cancer (CRC). While conditions such as Familial Adenomatous Polyposis and Lynch syndrome have well defined genetic causes, the search for variants underlying the remainder of familial CRC is plagued by genetic heterogeneity. The recent identification of families with a heritable predisposition to malignancies arising through the serrated pathway (familial serrated neoplasia or Jass syndrome) provides an opportunity to study a subset of familial CRC in which heterogeneity may be greatly reduced. A genome-wide linkage screen was performed on a large family displaying a dominantly-inherited predisposition to serrated neoplasia genotyped using the Affymetrix GeneChip Human Mapping 10 K SNP Array. Parametric and nonparametric analyses were performed and resulting regions of interest, as well as previously reported CRC susceptibility loci at 3q22, 7q31 and 9q22, were followed up by finemapping in 10 serrated neoplasia families. Genome-wide linkage analysis revealed regions of interest at 2p25.2-p25.1, 2q24.3-q37.1 and 8p21.2-q12.1. Finemapping linkage and haplotype analyses identified 2q32.2-q33.3 as the region most likely to harbour linkage, with heterogeneity logarithm of the odds (HLOD) 2.09 and nonparametric linkage (NPL) score 2.36 (P = 0.004). Five primary candidate genes (CFLAR, CASP10, CASP8, FZD7 and BMPR2) were sequenced and no segregating variants identified. There was no evidence of linkage to previously reported loci on chromosomes 3, 7 and 9

Microbial colonisation of human follicular fluid and adverse in vitro fertilisation outcomes

This study, investigating 263 women undergoing trans-vaginal oocyte retrieval for in vitro fertilisation (IVF) found that microorganisms colonising follicular fluid contributed to adverse IVF (pre-implantation) and pregnancy (post-implantation) outcomes including poor quality embryos, failed pregnancy and early pregnancy loss (< 37 weeks gestation). Some microorganisms also showed in vitro growth patterns in liquid media that appeared to be enhanced by the hormonal stimulation protocol used for oocyte retrieval. Elaborated cytokines within follicular fluid were also associated with adverse IVF outcomes. This study is imperative because infertility affects 16% of the human population and the numbers of couples needing assistance continues to increase. Despite significant improvements in the technical aspects of assisted reproductive technologies (ART), the live birth rate has not increased proportionally. Overt genital tract infection has been associated with both infertility and adverse pregnancy outcomes (including miscarriage and preterm birth) as a direct result of the infection or the host response to it. Importantly, once inflammation had become established, medical treatment often failed to prevent these significant adverse outcomes. Current evaluations of fertility focus on the ovary as a site of steroid hormone production and ovulation. However, infertility as a result of subclinical colonisation of the ovary has not been reported. Furthermore, identification of the microorganisms present in follicular fluid and the local cytokine profile may provide clinicians with an early indication of the prognosis for IVF treatment in infertile couples, thus allowing antimicrobial treatment and/or counselling about possible IVF failure. During an IVF cycle, multiple oocytes undergo maturation in vivo in response to hormonal hyperstimulation. Oocytes for in vitro insemination are collected trans-vaginally. The follicular fluid that bathes the maturing oocyte in vivo, usually is discarded as part of the IVF procedure, but provides a unique opportunity to investigate microbial causes of adverse IVF outcomes. Some previous studies have identified follicular fluid markers that predict IVF pregnancy outcomes. However, there have not been any detailed microbiological studies of follicular fluid. For this current study, paired follicular fluid and vaginal secretion samples were collected from women undergoing IVF cycles to determine whether microorganisms in follicular fluid were associated with adverse IVF outcomes. Microorganisms in follicular fluid were regarded as either "colonisers" or "contaminants"; colonisers, if they were unique to the follicular fluid sample, and contaminants if the same microorganisms were detected in the vaginal and follicular fluid samples indicating that the follicular fluid was merely contaminated during the oocyte retrieval process. Quite unexpectedly, by these criteria, we found that follicular fluid from approximately 30% of all subjects was colonised with bacteria. Fertile and infertile women with colonised follicular fluid had decreased embryo transfer rates and decreased pregnancy rates compared to women with contaminated follicular fluids. The observation that follicular fluid was not always sterile, but contained a diverse range of microorganisms, is novel. Many of the microorganisms we detected in follicular fluid are known opportunistic pathogens that have been detected in upper genital tract infections and are associated with adverse pregnancy outcomes. Bacteria were able to survive for at least 28 weeks in vitro, in cultures of follicular fluid. Within 10 days of establishing these in vitro cultures, several species (Lactobacillus spp., Bifidobacterium spp., Propionibacterium spp., Streptococcus spp. and Salmonella entericus) had formed biofilms. Biofilms play a major role in microbial pathogenicity and persistence. The propensity of microbial species to form biofilms in follicular fluid suggests that successful treatment of these infections with antimicrobials may be difficult. Bifidobacterium spp. grew, in liquid media, only if concentrations of oestradiol and progesterone were similar to those achieved in vivo during an IVF cycle. In contrast, the growth of Streptococcus agalactiae and Escherichia coli was inhibited or abolished by the addition of these hormones to culture medium. These data suggest that the likelihood of microorganisms colonising follicular fluid and the species of bacteria involved is influenced by the stage of the menstrual cycle and, in the case of IVF, the nature and dose of steroid hormones administered for the maturation of multiple oocytes in vivo. Our findings indicate that the elevated levels of steroid hormones during an IVF cycle may influence the microbial growth within follicular fluid, suggesting that the treatment itself will impact on the microflora present in the female upper genital tract during pre-conception and early post-conception phases of the cycle. The effect of the host immune response on colonising bacteria and on the outcomes of IVF also was investigated. White blood cells reportedly compose between 5% and 15% of the cell population in follicular fluid. The follicular membrane is semi-permeable and cells are actively recruited as part of the normal menstrual cycle and in response to microorganisms. A previous study investigated follicular fluid cytokines from infertile women and fertile oocyte donors undergoing IVF, and concluded that there were no significant differences in the cytokine concentrations between the two groups. However, other studies have reported differences in the follicular fluid cytokine levels associated with infertile women with endometriosis or polycystic ovary syndrome. In this study, elevated levels of interleukin (IL)-1 á, IL-1 â and vascular endothelial growth factor (VEGF) in vaginal fluid were associated with successful fertilisation, which may be useful marker for successful fertilisation outcomes for women trying to conceive naturally or prior to oocyte retrieval for IVF. Elevated levels of IL-6, IL-12p40, granulocyte colony stimulating factor (GCSF) and interferon-gamma (IFN ã) in follicular fluid were associated with successful embryo transfer. Elevated levels of pro-inflammatory IL-18 and decreased levels of anti-inflammatory IL-10 were identified in follicular fluid from women with idiopathic infertility. Successful fertilisation and implantation is dependent on a controlled pro-inflammatory environment, involving active recruitment of pro-inflammatory mediators to the genital tract as part of the menstrual cycle and early pregnancy. However, ongoing pregnancy requires an enhanced anti-inflammatory environment to ensure that the maternal immune system does not reject the semi-allergenic foetus. The pro-inflammatory skew in the follicular fluid of women with idiopathic infertility, correlates with normal rates of fertilisation, embryo discard and embryo transfer, observed for this cohort, which were similar to the outcomes observed for fertile women. However, their pregnancy rate was reduced compared to fertile women. An altered local immune response in follicular fluid may provide a means of explaining infertility in this cohort, previously defined as 'idiopathic'. This study has found that microorganisms colonising follicular fluid may have contributed to adverse IVF and pregnancy outcomes. Follicular fluid bathes the cumulus oocyte complex during the in vivo maturation process, and microorganisms in the fluid, their metabolic products or the local immune response to these microorganisms may result in damage to the oocytes, degradation of the cumulus or contamination of the IVF culture system. Previous studies that have discounted bacterial contamination of follicular fluid as a cause of adverse IVF outcomes failed to distinguish between bacteria that were introduced into the follicular fluid at the time of trans-vaginal oocyte retrieval and those that colonised the follicular fluid. Those bacteria that had colonised the fluid may have had time to form biofilms and to elicit a local immune response. Failure to draw this distinction has previously prevented consideration of bacterial colonisation of follicular fluid as a cause of adverse IVF outcomes. Several observations arising from this study are of significance to IVF programs. Follicular fluid is not always sterile and colonisation of follicular fluid is a cause of adverse IVF and pregnancy outcomes. Hormonal stimulation associated with IVF may influence whether follicular fluid is colonised and enhance the growth of specific species of bacteria within follicular fluid. Bacteria in follicular fluid may form biofilms and literature has reported that this may influence their susceptibility to antibiotics. Monitoring the levels of selected cytokines within vaginal secretions may inform fertilisation outcomes. This study has identified novel factors contributing to adverse IVF outcomes and that are most likely to affect also natural conception outcomes. Early intervention, possibly using antimicrobial or immunological therapies may reduce the need for ART and improve reproductive health outcomes for all women

Modélisation des effets des systèmes de culture et de leur répartition spatiale sur le phoma du colza et l'adaptation des populations pathogènes responsables de la maladie (Leptosphaeria maculans) aux résistances variétales.

One of the main control methods to manage phoma stem canker is the use of cultivars with specific or quantitative resistances. However, specific resistances lack durability. Other control methods can be used to manage the disease: chemical and cultural control methods (tillage to limit the quantity of primary inoculum on infected stubble, adaptation of the sowing date and rate, organic nitrogen supply to limit crop's receptivity to infections). The spatial and temporal combination of genetic, cultural and chemical control methods in a region makes it possible to better control the disease, to preserve the efficiency of specific resistant cultivars as well as economic profit for farmers, and to satisfy environmental and toxicological exigencies of integrated crop management. Given the considered scales and the number of technical operations that have to be taken into account, experiments are difficult, or simply impossible to set up to test control strategies. A model has been developed to test cropping systems that address these issues: SIPPOM-WOSR, a Simulator for Integrated Pathogen Population Management, for Winter OilSeed Rape. SIPPOM consists of 5 sub-models simulating i) primary inoculum production, ii) ascospore dispersal, iii) crop growth and attainable yield, iv) dynamics of pathogen population genetic structure, and v) infection and relative yield loss. Output variables are disease severity index and the associated yield loss, yield, gross margin, energetic cost of cultural practices and Treatments Frequency Index, as well as the genetic structure of pathogen populations, under the effect of four evolutionary forces (migration, selection, recombination, and Allee effect). An experiment has been set up to collect data on disease recurrence, and formalisms, as effect of quantitative resistance on disease severity or attainable yield calculation, have been completed with data from other experimentations. A sensitivity analysis has been carried out to study the sensitivity of sub-models to parameter variations. Examples of simulation illustrate how SIPPOM can be used to test integrated and durable disease control strategies.Une méthode de lutte efficace contre le phoma du colza est l'utilisation de variétés résistantes mais l'efficacité des résistances spécifiques est peu durable. D'autres méthodes de lutte peuvent être mobilisées : lutte chimique et contrôle cultural (adaptation du travail du sol, de la date et de la densité de semis, ou de l'azote organique). La combinaison spatiale et temporelle des méthodes de lutte génétique, culturale et chimique dans le paysage permet de mieux contrôler la maladie et de préserver l'efficacité des résistances spécifiques et la rentabilité économique, tout en répondant aux exigences environnementales et toxicologiques de la production intégrée. Etant données les échelles d'espace et de temps considérées et la multiplicité des techniques, il est difficile de tester expérimentalement ces stratégies. SIPPOM-WOSR a donc été développé, a Simulator for Integrated Pathogen Population Management, for Winter OilSeed Rape. Il est composé de 5 modules simulant la production d'inoculum, la dispersion des ascospores, la croissance du peuplement végétal et le rendement accessible, l'évolution de la structure génétique des populations pathogènes, et l'infection. Les sorties sont l'indice de sévérité de la maladie et les pertes de rendement associées, le rendement, la marge brute, le coût énergétique des pratiques et l'indice de fréquence de traitement, ainsi que la structure des populations pathogènes, sous l'effet de forces évolutives. Des expérimentations et analyses de données ont été réalisées pour acquérir des connaissances et compléter des formalismes, par exemple sur la récurrence de l'épidémie ou sur l'effet de la résistance quantitative sur la sévérité de la maladie. Une analyse de sensibilité a été réalisée pour étudier la sensibilité des différents modules aux variations des paramètres. Des exemples de simulation montrent l'intérêt de SIPPOM pour tester des stratégies de gestion intégrée et durable d'une maladie

Tubal damage, infertility and tubal ectopic pregnancy: Chlamydia trachomatis and other microbial aetiologies

Infertility is a worldwide health problem with one in six couples suffering from this condition and with a major economic burden on the global healthcare industry. Estimates of the current global infertility rate suggest that 15% of couples are infertile (Zegers-Hochschild et al 2009) defined as: (1) failure to conceive after 12 months of unprotected sexual intercourse (i.e. infertility); (2) repeated implantation failure following ART cycles; or (3) recurrent miscarriage without difficulty conceiving (natural conceptions). Tubal factor infertility is among the leading causes of female factor infertility accounting for 7-9.8% of all female factor infertilities. Tubal disease directly causes from 36% to 85% of all cases of female factor infertility in developed and developing nations respectively and is associated with polymicrobial aetiologies. One of the leading global causes of tubal factor infertility is thought to be symptomatic (and asymptomatic in up to 70% cases) infection of the female reproductive tract with the sexually transmitted pathogen, Chlamydia trachomatis. Infection-related damage to the Fallopian tubes caused by Chlamydia accounts for more than 70% of cases of infertility in women from developing nations such as sub-Saharan Africa (Sharma et al 2009). Bacterial vaginosis, a condition associated with increased transmission of sexually transmitted infections including those caused by Neisseria gonorrhoeae and Mycoplasma genitalium is present in two thirds of women with pelvic inflammatory disease (PID). This review will focus on (1) the polymicrobial aetiologies of tubal factor infertility and (2) studies involved in screening for, and treatment and control of, Chlamydial infection to prevent PID and the associated sequelae of Fallopian tube inflammation that may lead to infertility and ectopic pregnancy

A global experimental dataset for assessing grain legume production

Grain legume crops are a significant component of the human diet and animal feed and have an important role in the environment, but the global diversity of agricultural legume species is currently underexploited. Experimental assessments of grain legume performances are required, to identify potential species with high yields. Here, we introduce a dataset including results of field experiments published in 173 articles. The selected experiments were carried out over five continents on 39 grain legume species. The dataset includes measurements of grain yield, aerial biomass, crop nitrogen content, residual soil nitrogen content and water use. When available, yields for cereals and oilseeds grown after grain legumes in the crop sequence are also included. The dataset is arranged into a relational database with nine structured tables and 198 standardized attributes. Tillage, fertilization, pest and irrigation management are systematically recorded for each of the 8,581 crop* field site* growing season* treatment combinations. The dataset is freely reusable and easy to update. We anticipate that it will provide valuable information for assessing grain legume production worldwide