Ultra pure high molecular weight DNA from soil for Nanopore shotgun metagenomics and metabarcoding sequencing

Soil microbes are among the most abundant and diverse organisms on Earth but remain poorly characterized. New technologies have made possible to sequence the DNA of uncultivated microorganisms in soil and other complex ecosystems. Genome assembly is crucial for understanding their functional potential. Nanopore sequencing technologies allow to sequence long DNA fragments, optimizing production of metagenome-assembled genomes compared to short-read technology. Extracting DNA with a very high purity and high molecular weight is key to get the most out of this long read technologies. Here we present two extraction protocols to get DNA with high purity. First protocol is optimized to reach DNA quality suiting Nanopore shotgun metagenomics. It uses a non-toxic centrifugation gradient to separate bacterial cells from soil to extract DNA directly on cells. The median length of the acquired DNA sequences (N50) was 3 to 7 times greater than previously published in the literature, achieving an N50 of ∼14 kb. The other, a modification of a commercially available MP Biomedical DNA extraction kit, yielded high-purity DNA for full-length 16S Oxford Nanopore metabarcoding, with an N50 of ∼8 kb. The MP-based protocol achieves higher yields of ultra-pure DNA compared to the Nycodenz protocol, at the expense of shorter fragment lengths

Mycorrhization of fagaceae forests within mediterranean ecosystems

Mediterranean Fagaceae forests are valuable due to their ecological and socioeconomic aspects. Some profitable plant species, such as Castanea (timber and chestnut), Quercus (timber and cork), and Fagus (timber), encounter in this habitat the excellent edaphoclimatic conditions to develop. All Fagaceae plants are commonly associated to ECM fungal species, which are found in these forests in quite stable communities, mainly enriched in Russulaceae and Telephoraceae species. Currently, the Mediterranean Basin is considered as one of the global biodiversity hotspots, since many of their endemic plant species are not found elsewhere and are now under threat. Due to climate changing and introduction of disease agents, Fagaceae forests are facing an adaptation challenge to both biotic and abiotic threats. Although ECM communities are highly disturbed by climate factors and tree disease incidence, they could play an important role in increasing water availability to the plant and also improving plant tree defense against pathogens. Recent advances, namely, on genomics and transcriptomics, are providing tools for increasing the understanding of Fagaceae mycorrhization process and stress responses to biotic and abiotic stresses. Such studies can provide new information for the implementation of the most adequate management policies for protecting threaten Mediterranean forests.info:eu-repo/semantics/publishedVersio

Efficiency of the traditional practice of traps to stimulate black truffle production, and its ecological mechanisms

The black truffle Tuber melanosporum was disseminated all over the world, propelled by the development of a wide variety of empirical practices. A widespread practice, called ‘truffle trap’, consists of placing pieces of truffles into excavations dug under host trees, and of collecting truffle in these traps in the next years. This research aims at (1) evaluating the effect of this practice on fruitbody production based on the analysis of 9924 truffle traps installed in 11 orchards across T. melanosporum native area in France and (2) exploring the mechanisms involved in fruitbody emergence using traps where the genotypes of introduced truffles were compared with those of fruitbodies collected in the same traps. We confirmed that truffle traps provide a major and highly variable part of truffle ground production, representing up to 89% of the collected fruitbodies. We evidenced a genetic link between introduced spores and collected fruitbodies, and then demonstrated that truffle growers provide paternal partners for mating with local maternal mycelia. We also highlighted that soil disturbance stimulate the vegetative development of established maternal mycelia. This research supports that a widely used traditional practice enhances fruitbody production by shaping favorable conditions and providing sexual partners required for fruiting.info:eu-repo/semantics/publishedVersio

Discovery of long-distance gamete dispersal in a lichen-forming ascomycete

Accurate estimates of gamete and offspring dispersal range are required for the understanding and prediction of spatial population dynamics and species persistence. Little is known about gamete dispersal in fungi, especially in lichen-forming ascomycetes. Here, we estimate the dispersal functions of clonal propagules, gametes and ascospores of the epiphytic lichen Lobaria pulmonaria. We use hierarchical Bayesian parentage analysis, which integrates genetic and ecological information from multiannual colonization and dispersal source data collected in a large, oldgrowth forest landscape. The effective dispersal range of gametes is several hundred metres to kilometres from potential paternal individuals. By contrast, clonal propagules disperse only tens of metres, and ascospores disperse over several thousand metres. Our study reveals the dispersal distances of individual reproductive units; clonal propagules, gametes and ascospores, which is of great importance for a thorough understanding of the spatial dynamics of ascomycetes. Sexual reproduction occurs between distant individuals. However, whereas gametes and ascospores disperse over long distances, the overall rate of colonization of trees is low. Hence, establishment is the limiting factor for the colonization of new host trees by the lichen in old- growth landscapes.Peer reviewe

Sculpture: From the renaissance to the Present Day from the fifteenth to the twentirth century (part 3)

Mulai dari patung kuno sampai kontemporer, buku ini merupakan studi pertama sejarah patung untuk menyajikan pendekatan yang orisinil dan menyeluruh. Mengambil patung-patung dari konteks museum (dan dengan demikian terlepas dari tiang pepatah mereka), buku ini menyajikan pandangan yang sama sekali baru yang memberikan perbandingan yang mencerahkan antara era dan genre. Karya yang luar biasa ini sangat diperlukan untuk pecinta seni dari semua selera dan disiplin ilmu. Penulis yang berkontribusi Xavier Barral I Altet, Geneviève Bresc-Bautier, Philippe Bruneau, Bernard Ceysson, Jean-Luc Daval, Georges Duby, Maurizio Fagiolo dell'Arco, Sophie Guillot de Suduiraut, Reinhold Hohl, Antoinette Le Normand-Romain, Friedrich Meschede, Anne Pingeot, Barbara Rose, François Souchal, dan Mario Torelli

Biotic interactions and reproductive biology of the Black Truffle (Tuber melanosporum Vittad.) : from spontaneous to planted truffle grounds

La Truffe noire (Tuber melanosporum Vittad.) est un champignon ectomycorhizien spontanément présent dans les groupements végétaux ouverts en cours de reforestation. Alors que ces milieux ont fortement régressé au XXème siècle dans la zone méditerranéenne, 80 % de la production actuelle provient de boisements artificiels où des arbres inoculés par la Truffe sont plantés. Malgré un grand corpus de connaissances empiriques, la production reste souvent aléatoire et les connaissances fondamentales d'écologie et de biologie de la Truffe restent fragmentaires. Dans ce travail, nous avons d'abord étudié la distribution de la diversité fongique ectomycorhizienne sur les différents hôtes présents dans les garrigues pré-forestières à Truffe. Nous avons ensuite testé les interactions entre la Truffe et les plantes endo- ou non-mycorhiziennes, qui se matérialisent par la création d'un brûlé, où la flore est localement affectée. Dans un troisième volet, nous avons cherché à mieux comprendre la diversité génétique des populations de Truffes, et plus spécifiquement l'appariement sexuel et la dispersion de cette espèce à vie végétative haploïde et à fructification hypogée. Par une approche comparative entre truffières plantées et spontanées, nous avons finalement évalué les modifications liées au processus de proto-domestication en cours. Ainsi, en combinant écologie des communautés, expériences en conditions contrôlées et génétique des populations, nous avons montré qu'en région méditerranéenne :1) La Truffe est présente de façon fugace dans des communautés ectomycorhiziennes riches, avec de nombreuses espèces multi-hôtes, mais où la Truffe montre une préférence d'hôte marquée pour le chêne vert (Q. ilex). 2) Certaines plantes endo- ou non-mycorhiziennes, dont l'effet positif sur la Truffe a empiriquement été observé par les trufficulteurs, favorisent le développement du mycélium de Truffe dans le sol, agissant indirectement sur les interactions plante-plante (chêne – plantes endomycorhiziennes). L'effet inhibiteur de la Truffe observé sur la germination des graines peut-être une des causes précoces du brûlé. Par ailleurs, la Truffe semble effectivement coloniser les racines de plantes herbacées non-ectomycorhiziennes.3) Les flux de gènes sont limités à l'échelle de la truffière, l'appariement sexuel réunit des individus proches génétiquement et physiquement, et bien que la Truffe soit probablement hermaphrodite, les parents paternels sont peu détectables, probablement de taille plus réduite que les parents maternels (formant la gléba). Les pratiques culturales pourraient entraîner un brassage génétique plus important en plantation, mais à l'échelle régionale, aucune différence de diversité génétique n'a été détectée entre populations spontanées et cultivées. Ce travail montre la richesse des interactions biotiques impliquant la Truffe et les diversités végétale et fongique des truffières artificielles et spontanées de la région méditerranéenne. Les résultats acquis contribuent à lever le voile sur sa biologie reproductive, et jalonnent le chemin pour des pratiques intégratrices de la diversité biologique des truffières, ainsi que pour le développement de futures expérimentations in situ. Mots clés : appariement sexuel, Arbutus unedo, Cistus albidus, domestication, écologie des communautés, forêts méditerranéennes, génétique des populations, isolement par la distance, ITS, microsatellites, mésocosmes, mycorhizes, pratiques empiriques, qPCR, Quercus coccifera, Quercus ilex, successions secondairesThe Black Truffle (Tuber melanosporum Vittad.) is an ectomycorrhizal fungus spontaneously growing in open woodlands before canopy closure. Such open landscapes drastically regressed during the last century in the Mediterranean regions, and nowadays 80% of the production comes from man-made plantations where the Truffle is inoculated. Despite a large corpus of local knowledge and empirical practices, the production remains largely sporadic and unpredictable, and our knowledge of the biology and ecology of the Truffle is still fragmentary. In this work, we first analyzed the distribution of the ectomycorrhizal fungal diversity among host plants co-existing in the shrub-dominated landscapes where Truffle naturally occurs. We then analyzed the interactions between the Truffle and endo- or non-mycorrhizal plants, as they typically occur in the so-called brûlés, zones with scarce vegetation. A third part aimed at better understanding the genetic diversity of Truffle populations, with special focus on fertilization and dispersal process of this fungus with haploid lifecycle and hypogeous fruiting. In a multi-scale approach combining community ecology, experimentation and population genetics, we found that in the Mediterranean region:1) The Truffle is transiently present in rich ectomycorrhizal communities, showing a significant host preference for Q. ilex, in assemblies made of numerous multi-host fungal species. 2) Some endo- or non-mycorrhizal plants species, that were supposed to provide beneficial effect on the Truffle, can be experimentally shown to stimulate the development of T. melanosporum mycelium in soil, and indirectly trigger plant-plant interactions (between oak and endomycorrhizal plants). The early brûlé symptoms could at least partially result from a Truffle's inhibitor effect on seed germination.3) At truffle ground scale, gene flow is limited, and mating occurs between genetically and physically close parents. Despite probable hermaphroditism of the Truffle, paternal parents are poorly detectable, certainly of smaller size than maternal ones (these forming nourishing tissue of the ascocarp). Cultural practices could favor genetic mixing/diversity at brûlé scale, but at the regional scale, no difference in genetic diversity was found between spontaneous and planted compartments.This work revealed the richness of biotic interactions involving the black Truffle and the plant as well as the fungal diversity in both artificial and spontaneous truffle-ground of the Mediterranean region. These results enlighten the reproductive biology of the species, and pave the way for practices integrating the biological diversity of truffle-grounds and the development of further in situ experimentations. Key words: Arbutus unedo, Cistus albidus, community ecology, domestication, empirical practices, local knowledge, experimental approach, inbreeding, isolation by distance, ITS, Mediterranean forests, mesocosms, microsatellites, mycorrhiza, population genetics, qPCR, Quercus ilex, Q. coccifera, secondary successions

Bercelona: Shops & More

Buku ini berisi informasi tempat-tempat perbelanjaan di kota Bercelona. Buku ini dibagi menjadi 3 bagian; El Raval, Barri Gotic El Born La Ribera dan L'Eixample Gracia sant Gervasi. El raval berisi tulisan tentang: market hall, coffee roasters, architectural & art books, bakery, herbalst, haberdashery & interior & cooks 'apparel. Barri Gotic El Born La Ribera berisi tentang; chocholate shope, boutique & tea salon, candles & devotional articles dll. Sedangkan L'Eixample Graca Sant Gervasi berisi tentang travel books,Spanish leather goods, Spanish fashion dan masih banyak artikel lain

Tuber melanosporum datasets from Taschen et al. 2016

<p>3 genetic datasets in genepop (.gen) or GenAlEx format (.csv) :</p> <ul> <li>"zygotes_SB1.gen"= genepop file containing 20 "diploid" individuals genotyped with 13 SSR markers, in one sampling site (SB1)</li> <li>"zygotes_SB2.gen"  = genepop file containing 10 "diploid" individuals genotyped with 13 SSR markers, in one sampling site (SB2)</li> <li>"SB1.csv" = GenAlEx file containing 19 haploid individuals genotyped with 11SSR markers, in one sampling site (SB1)</li> <li>"SB2.csv" = GenAlEx file containing 13 haploid individuals genotyped with 11SSR markers, in one sampling site (SB2)</li> </ul&gt