Macroinvertebrate community traits and nitrate removal in stream sediments

1. In-stream nitrate removal capacity may be used as a proxy for the ecosystem service of water quality regulation. It is well known that this natural function is driven by abiotic and biotic factors in running water environments. With regard to biotic drivers, most of the literature focuses on the microbial community influences, but there has been very little emphasis on the relationship with the benthic macroinvertebrate community. Since this community feeds on microbial assemblages (autotrophic and/or heterotrophic biofilms) that live on the streambed and in the hyporheic zone of the river, macroinvertebrates also have the potential to influence nitrate removal via its influences on microbiological processes.2. The objective of this study was to examine the potential relationship between the macroinvertebrate communities and nitrate removal. A dataset of in-stream nitrate removal rates measured in nine-third-order streams was analysed. The simultaneous influences of abiotic (hydromorphological, physical and chemical characteristics) and biotic (biofilm and macroinvertebrate) drivers were examined and together explained 56% of the in-stream nitrate removal variance. An analysis of the independent contributions of each driver showed that abiotic drivers (e.g. ammonium, dissolved organic carbon, temperature and transient zone) contributed 40% of this nitrate removal variance, whereas the macroinvertebrate community contributed 39%.3. The potential relationship between macroinvertebrates and nitrate removal was subsequently explored using trait-based approaches of the macroinvertebrate community. This method allows for the selection of trait modalities assuming a top-down control of microbial communities by macroinvertebrates, with in-stream abiotic conditions correlated with nitrate removal (assuming that environmental conditions affect macroinvertebrate community composition).4. The main trait modalities positively correlated with nitrate removal were scraper (feeding habit), flagstones/boulders/cobbles/pebbles (substrate preference), crawler and interstitial (locomotion) and detritus (food). The main modalities negatively correlated with nitrate removal were silt and mud with microphytes (as substrate preference), and with fine sediment with microorganisms, and dead animals (as food sources). These results agreed with the hypothesis of top-down control and enhanced understanding of the influence of hydromorphological factors on nitrate removal.5. This study highlights the involvement of the macroinvertebrate community in in-stream nitrate processing, and demonstrates the usefulness of applying a functional approach to explain relationships between biodiversity and ecosystem function

Scale dependency in the hydromorphological control of a stream ecosystem functioning

Physical habitat degradation is prevalent in river ecosystems. Although still little is known about the ecological consequences of altered hydromorphology, understanding the factors at play can contribute to sustainable environmental management. In this study we aimed to identify the hydromorphological features controlling a key ecosystem function and the spatial scales where such linkages operate. As hydromorphological and chemical pressures often occur in parallel, we examined the relative importance of hydromorphological and chemical factors as determinants of leaf breakdown. Leaf breakdown assays were investigated at 82 sites of rivers throughout the French territory. Leaf breakdown data were then crossed with data on water quality and with a multi-scale hydro- morphological assessment (i.e. upstream catchment, river segment, reach and habitat) when quantitative data were available. Microbial and total leaf breakdown rates exhibited differential responses to both hydromorphological and chemical alterations. Relationships between the chemical quality of the water and leaf breakdown were weak, while hydromorphological integrity explained independently up to 84.2% of leaf breakdown. Hydrological and morphological parameters were the main predictors of microbial leaf breakdown, whereas hydrological parameters had a major effect on total leaf breakdown, particularly at large scales, while morphological parameters were important at smaller scales. Microbial leaf breakdown were best predicted by hydromorphological features defined at the upstream catchment level whereas total leaf breakdown were best predicted by reach and habitat level geomorphic variables. This study demonstrates the use of leaf breakdown in a biomonitoring context and the importance of hydromorphological integrity for the functioning of running water. It provides new insights for envi- ronmental decision-makers to identify the management and restoration actions that have to be un- dertaken including the hydromorphogical features that should be kept in minimal maintenance to support leaf breakdown

Novel insights into the diet of the Pyrenean desman (Galemys pyrenaicus) using next-generation sequencing molecular analyses

[Departement_IRSTEA]EauxInternational audienceThe Pyrenean desman, a threatened, semiaquatic mammal, is considered a specialist predator feeding on aquatic benthic invertebrates. This categorization comes from visual identification of prey in scat or gut contents, often based on a limited number of samples and locations. We combined diet analyses using next-generation sequencing methods with an extensive survey to explore the summer diet of Pyrenean desmans across the French Pyrenees. This study thus provides an unprecedented level of detail on the trophic ecology of Pyrenean desmans. Our results revealed a diverse diet containing a high proportion of rare prey and substantial consumption of terrestrial prey, which suggests a more generalist diet than previously understood. Three diet groups were identified, with significant differences in prey composition. These differences were not related to geographic location, but rather to local environmental variables. The spatial variation in diet was likely induced by local abiotic parameters that affect prey availability or use of foraging habitats

Le gisement paléolithique multistratifié « les Bossats » à Ormesson (Seine-et-Marne, France) : palethnographie ou pâle ethnographie ? Une synthèse des huit premières années de fouille (2009-2016)

editorial reviewedÀ l'évidence, ces vingt dernières années ont vu en France, notamment, se développer en parallèle deux nouvelles façons de traiter le Paléolithique supérieur ancien qui ne sont pas antagonistes d'ailleurs. L'une consiste en une reprise des stratigraphies anciennes dans le Centre et le Sud-Ouest de la France plus spécifiquement et est associée à une meilleure redéfinition des entités culturelles par l'analyse détaillée des différentes composantes des systèmes techniques. L'autre s'efforce d'appliquer à cette période la démarche palethnographique, inféodée historiquement au Magdalénien du Bassin parisien. Il est vrai que peu de gisements autorisaient ce type d'approche, en raison d'une surface fouillée insuffisante ou d'un état de conservation médiocre, mais même lorsque les découvertes s'y prêtaient, le manque de temps et d'investissement freinait également toute velléité d'une étude approfondie des sites en question, qui aurait alors débouché sur une lecture palethnographique des lieux et des artefacts. À l'issue d'un PCR mené entre 1999 et 2005, nous pouvions ainsi légitimement nous demander si nous étions capables de jouer les ethnologues du passé pour le Paléolithique supérieur ancien dans le Bassin parisien. Les sites identifiés dans le cadre de ce programme de recherche étaient certes nombreux mais représentés surtout par des découvertes de surface, ils ne garantissaient pas un niveau d'analyse digne de ce qui a pu se faire depuis plus de 50 ans à Pincevent ou à Étiolles par exemple (Bodu et al., 2013). Il aura fallu attendre la découverte fortuite du gisement de plein-air d'Ormesson « les Bossats » (Seine-et-Marne, près de Nemours) au début des années 2000 pour que cette question trouve une réponse positive. Concernant, au départ, presqu'exclusivement des vestiges lithiques et osseux attribués au Gravettien, les premières fouilles menées en 2009 permirent d'identifier rapidement un second niveau d'occupation, d'attribution moustérienne. Les campagnes suivantes amenèrent à la découverte de cinq autres niveaux d'occupation paléolithiques, inégaux tant pour la surface couverte que pour l'état de conservation : un second niveau moustérien résultant vraisemblablement de palimpsestes, un ensemble châtelperronien, un autre solutréen, un quatrième badegoulien et enfin entre Châtelperronien et Gravettien, un foyer isolé sans vestiges archéologiques associés. Cette stratigraphie paléolithique de plein-air dilatée est le témoignage d'une forte occupation du lieu pendant près de 30 000 ans, ce qui s'explique notamment par la configuration particulière de la vallée à cet endroit. À la diversité chronologique des occupations préhistoriques répond une diversité des comportements économiques et techniques au sein des différentes sphères d'activités mais également des habitudes spatiales différentes. À l'issue des huit premières années de fouille (2009-2016), le site d'Ormesson « les Bossats » permet ainsi de développer une approche détaillée des comportements techniques, économiques, spatiaux de groupes culturels distincts ayant vécu durant 30 000 ans dans un cadre géomorphologique et plus globalement naturel, relativement identique. Dépassant le jeu de mot facile « palethnographie ou pâle ethnographie ? » à Ormesson « les Bossats », nous proposons ici quelques éléments de réponse

Global Patterns and Controls of Nutrient Immobilization On Decomposing Cellulose In Riverine Ecosystems

Microbes play a critical role in plant litter decomposition and influence the fate of carbon in rivers and riparian zones. When decomposing low-nutrient plant litter, microbes acquire nitrogen (N) and phosphorus (P) from the environment (i.e., nutrient immobilization), and this process is potentially sensitive to nutrient loading and changing climate. Nonetheless, environmental controls on immobilization are poorly understood because rates are also influenced by plant litter chemistry, which is coupled to the same environmental factors. Here we used a standardized, low-nutrient organic matter substrate (cotton strips) to quantify nutrient immobilization at 100 paired stream and riparian sites representing 11 biomes worldwide. Immobilization rates varied by three orders of magnitude, were greater in rivers than riparian zones, and were strongly correlated to decomposition rates. In rivers, P immobilization rates were controlled by surface water phosphate concentrations, but N immobilization rates were not related to inorganic N. The N:P of immobilized nutrients was tightly constrained to a molar ratio of 10:1 despite wide variation in surface water N:P. Immobilization rates were temperature-dependent in riparian zones but not related to temperature in rivers. However, in rivers nutrient supply ultimately controlled whether microbes could achieve the maximum expected decomposition rate at a given temperature

Identification of a BRCA2-Specific modifier locus at 6p24 related to breast cancer risk

Common genetic variants contribute to the observed variation in breast cancer risk for BRCA2 mutation carriers; those known to date have all been found through population-based genome-wide association studies (GWAS). To comprehensively identify breast cancer risk modifying loci for BRCA2 mutation carriers, we conducted a deep replication of an ongoing GWAS discovery study. Using the ranked P-values of the breast cancer associations with the imputed genotype of 1.4 M SNPs, 19,029 SNPs were selected and designed for inclusion on a custom Illumina array that included a total of 211,155 SNPs as part of a multi-consortial project. DNA samples from 3,881 breast cancer affected and 4,330 unaffected BRCA2 mutation carriers from 47 studies belonging to the Consortium of Investigators of Modifiers of BRCA1/2 were genotyped and available for analysis. We replicated previously reported breast cancer susceptibility alleles in these BRCA2 mutation carriers and for several regions (including FGFR2, MAP3K1, CDKN2A/B, and PTHLH) identified SNPs that have stronger evidence of association than those previously published. We also identified a novel susceptibility allele at 6p24 that was inversely associated with risk in BRCA2 mutation carriers (rs9348512; per allele HR = 0.85, 95% CI 0.80-0.90, P = 3.9×10−8). This SNP was not associated with breast cancer risk either in the general population or in BRCA1 mutation carriers. The locus lies within a region containing TFAP2A, which encodes a transcriptional activation protein that interacts with several tumor suppressor genes. This report identifies the first breast cancer risk locus specific to a BRCA2 mutation background. This comprehensive update of novel and previously reported breast cancer susceptibility loci contributes to the establishment of a panel of SNPs that modify breast cancer risk in BRCA2 mutation carriers. This panel may have clinical utility for women with BRCA2 mutations weighing options for medical prevention of breast cancer

Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast-ovarian cancer susceptibility locus

A locus at 19p13 is associated with breast cancer (BC) and ovarian cancer (OC) risk. Here we analyse 438 SNPs in this region in 46,451 BC and 15,438 OC cases, 15,252 BRCA1 mutation carriers and 73,444 controls and identify 13 candidate causal SNPs associated with serous OC (P=9.2 × 10-20), ER-negative BC (P=1.1 × 10-13), BRCA1-associated BC (P=7.7 × 10-16) and triple negative BC (P-diff=2 × 10-5). Genotype-gene expression associations are identified for candidate target genes ANKLE1 (P=2 × 10-3) and ABHD8 (P<2 × 10-3). Chromosome conformation capture identifies interactions between four candidate SNPs and ABHD8, and luciferase assays indicate six risk alleles increased transactivation of the ADHD8 promoter. Targeted deletion of a region containing risk SNP rs56069439 in a putative enhancer induces ANKLE1 downregulation; and mRNA stability assays indicate functional effects for an ANKLE1 3′-UTR SNP. Altogether, these data suggest that multiple SNPs at 19p13 regulate ABHD8 and perhaps ANKLE1 expression, and indicate common mechanisms underlying breast and ovarian cancer risk

An original phylogenetic approach identified mitochondrial haplogroup T1a1 as inversely associated with breast cancer risk in BRCA2 mutation carriers

Introduction: Individuals carrying pathogenic mutations in the BRCA1 and BRCA2 genes have a high lifetime risk of breast cancer. BRCA1 and BRCA2 are involved in DNA double-strand break repair, DNA alterations that can be caused by exposure to reactive oxygen species, a main source of which are mitochondria. Mitochondrial genome variations affect electron transport chain efficiency and reactive oxygen species production. Individuals with different mitochondrial haplogroups differ in their metabolism and sensitivity to oxidative stress. Variability in mitochondrial genetic background can alter reactive oxygen species production, leading to cancer risk. In the present study, we tested the hypothesis that mitochondrial haplogroups modify breast cancer risk in BRCA1/2 mutation carriers. Methods: We genotyped 22,214 (11,421 affected, 10,793 unaffected) mutation carriers belonging to the Consortium of Investigators of Modifiers of BRCA1/2 for 129 mitochondrial polymorphisms using the iCOGS array. Haplogroup inference and association detection were performed using a phylogenetic approach. ALTree was applied to explore the reference mitochondrial evolutionary tree and detect subclades enriched in affected or unaffected individuals. Results: We discovered that subclade T1a1 was depleted in affected BRCA2 mutation carriers compared with the rest of clade T (hazard ratio (HR) = 0.55; 95% confidence interval (CI), 0.34 to 0.88; P = 0.01). Compared with the most frequent haplogroup in the general population (that is, H and T clades), the T1a1 haplogroup has a HR of 0.62 (95% CI, 0.40 to 0.95; P = 0.03). We also identified three potential susceptibility loci, including G13708A/rs28359178, which has demonstrated an inverse association with familial breast cancer risk. Conclusions: This study illustrates how original approaches such as the phylogeny-based method we used can empower classical molecular epidemiological studies aimed at identifying association or risk modification effects.Peer reviewe

The FANCM:p.Arg658* truncating variant is associated with risk of triple-negative breast cancer

Abstract: Breast cancer is a common disease partially caused by genetic risk factors. Germline pathogenic variants in DNA repair genes BRCA1, BRCA2, PALB2, ATM, and CHEK2 are associated with breast cancer risk. FANCM, which encodes for a DNA translocase, has been proposed as a breast cancer predisposition gene, with greater effects for the ER-negative and triple-negative breast cancer (TNBC) subtypes. We tested the three recurrent protein-truncating variants FANCM:p.Arg658*, p.Gln1701*, and p.Arg1931* for association with breast cancer risk in 67,112 cases, 53,766 controls, and 26,662 carriers of pathogenic variants of BRCA1 or BRCA2. These three variants were also studied functionally by measuring survival and chromosome fragility in FANCM−/− patient-derived immortalized fibroblasts treated with diepoxybutane or olaparib. We observed that FANCM:p.Arg658* was associated with increased risk of ER-negative disease and TNBC (OR = 2.44, P = 0.034 and OR = 3.79; P = 0.009, respectively). In a country-restricted analysis, we confirmed the associations detected for FANCM:p.Arg658* and found that also FANCM:p.Arg1931* was associated with ER-negative breast cancer risk (OR = 1.96; P = 0.006). The functional results indicated that all three variants were deleterious affecting cell survival and chromosome stability with FANCM:p.Arg658* causing more severe phenotypes. In conclusion, we confirmed that the two rare FANCM deleterious variants p.Arg658* and p.Arg1931* are risk factors for ER-negative and TNBC subtypes. Overall our data suggest that the effect of truncating variants on breast cancer risk may depend on their position in the gene. Cell sensitivity to olaparib exposure, identifies a possible therapeutic option to treat FANCM-associated tumors

Genome-Wide Association Study in BRCA1 Mutation Carriers Identifies Novel Loci Associated with Breast and Ovarian Cancer Risk

BRCA1-associated breast and ovarian cancer risks can be modified by common genetic variants. To identify further cancer risk-modifying loci, we performed a multi-stage GWAS of 11,705 BRCA1 carriers (of whom 5,920 were diagnosed with breast and 1,839 were diagnosed with ovarian cancer), with a further replication in an additional sample of 2,646 BRCA1 carriers. We identified a novel breast cancer risk modifier locus at 1q32 for BRCA1 carriers (rs2290854, P = 2.7×10-8, HR = 1.14, 95% CI: 1.09-1.20). In addition, we identified two novel ovarian cancer risk modifier loci: 17q21.31 (rs17631303, P = 1.4×10-8, HR = 1.27, 95% CI: 1.17-1.38) and 4q32.3 (rs4691139, P = 3.4×10-8, HR = 1.20, 95% CI: 1.17-1.38). The 4q32.3 locus was not associated with ovarian cancer risk in the general population or BRCA2 carriers, suggesting a BRCA1-specific associat