Potential uptake of dissolved organic matter by seagrasses and macroalgae

Dissolved organic nitrogen (DON) acts as a large reservoir of fixed nitrogen. Whereas DON utilization is common in the microbial community, little is known about utilization by macrophytes. We investigated the ability of the coexisting temperate marine macrophytes Zostera noltii, Cymodocea nodosa, and Caulerpa prolifera to take up nitrogen and carbon from small organic substrates of different molecular complexities (urea, glycine, L-leucine, and L-phenylalanine) and from dissolved organic matter (DOM) derived from algal and bacterial cultures (substrates with a complex composition). In addition to inorganic nitrogen, nitrogen from small organic substrates could be taken up in significant amounts by all macrophytes. Substrate uptake by the aboveground tissue differed from that of the belowground tissue. No relationships between carbon and nitrogen uptake of small organics were found. The preference for individual organic substrates was related to their structural complexity and C:N ratio. Uptake of algae-derived organic nitrogen was of similar magnitude as inorganic nitrogen, and was preferred over bacteria-derived nitrogen. These results add to the growing evidence that direct or quick indirect DON utilization may be more widespread among aquatic macrophytes than traditionally thought.This research was supported by the regional government of Andalusia project FUNDIV (P07-RNM-2516), the Spanish Project CTM2008-00012/MAR, a European Reintegration Grant (MERG-CT-2007-205675), a travel grant from Schure-Beijerinck-Popping Fund (SBP/JK/2007-32) and the Netherlands Organization for Scientific Research. Thanks to Fidel Echevarrìa Navas (Director of CACYTMAR) for granting us access to facilities, and to Bas Koutstaal for helping with sample processing. We also thank the anonymous reviewers for their valuable comments which significantly improved this manuscript

Morphological Trait Evolution in Solanum (Solanaceae): Evolutionary Lability of Key Taxonomic Characters

Solanum is one of the world\u27s largest and economically most important plant genera, including 1245 currently accepted species and several major and minor crops (e.g., tomato, potato, brinjal eggplant, scarlet eggplant, Gboma eggplant, lulo, and pepino). Here we provide an overview of the evolution of 25 key morphological traits for the major and minor clades of this giant genus based on stochastic mapping using a well-sampled recently published phylogeny of Solanum. The most evolutionarily labile traits (showing \u3e100 transitions across the genus) relate to plant structure (growth form and sympodial unit structure), herbivore defence (glandular trichomes), pollination (corolla shape and colour), and dispersal (fruit colour). Ten further traits show evolutionary lability with 50–100 transitions across the genus (e.g., specialised underground organs, trichome structure, leaf type, inflorescence position and branching, stamen heteromorphism). Our results reveal a number of highly convergent traits in Solanum, including tubers, rhizomes, simple leaves, yellow corollas, heteromorphic anthers, dioecy, and dry fruits, and some unexpected pathways of trait evolution that could be explored in future studies. We show that informally named clades of Solanum can be morphologically defined by trait combinations providing a tool for identification and enabling predictive phylogenetic placement of unsampled species

Effects of seagrasses and algae of the Caulerpa family on hydrodynamics and particle-trapping rates

The widespread decline of seagrass beds within the Mediterranean often results in the replacement of seagrasses by opportunistic green algae of the Caulerpa family. Because Caulerpa beds have a different height, stiffness and density compared to seagrasses, these changes in habitat type modify the interaction of the seafloor with hydrodynamics, influencing key processes such as sediment resuspension and particle trapping. Here, we compare the effects on hydrodynamics and particle trapping of Caulerpa taxifolia, C. racemosa, and C. prolifera with the Mediterranean seagrasses Cymodocea nodosa and Posidonia oceanica. All macrophyte canopies reduced near-bed volumetric flow rates compared to bare sediment, vertical profiles of turbulent kinetic energy revealed peak values around the top of the canopies, and maximum values of Reynolds stress increased by a factor of between 1.4 (C. nodosa) and 324.1 (P. oceanica) when vegetation was present. All canopies enhanced particle retention rates compared to bare sediment. The experimental C. prolifera canopy was the most effective at particle retention (m2 habitat); however, C. racemosa had the largest particle retention capacity per structure surface area. Hence, in terms of enhancing particle trapping and reducing hydrodynamic forces at the sediment surface, Caulerpa beds provided a similar or enhanced function compared to P.oceanica and C. nodosa. However, strong seasonality in the leaf area index of C. racemosa and C. taxifolia within the Mediterranean, combined with a weak rhizome structure, suggests that sediments maybe unprotected during winter storms, when most erosion occurs. Hence, replacement of seagrass beds with Caulerpa is likely to have a major influence on annual sediment dynamics at ecosystem scales.This research was funded by the European Network of Excellence ‘‘Marine Biodiversity and Ecosystem Function’’ (MarBEF); FP6, EC contract no. 505446 and a grant from the Fundacio ´n BBVA. EPM was supported by a European Union Marie Curie host fellowship for transfer of knowledge, MTKD-CT-2004-509254, the Spanish national project EVAMARIA (CTM2005-00395/MAR) and the regional government of Andalusia project FUNDIV(P07-RNM-2516)

Natural occurring epialleles determine vitamin E accumulation in tomato fruits

Vitamin E (VTE) content is a low heritability nutritional trait for which the genetic determinants are poorly understood. Here, we focus on a previously detected major tomato VTE quantitative trait loci (QTL; mQTL9-2-6) and identify the causal gene as one encoding a 2-methyl-6-phytylquinol methyltransferase (namely VTE3(1)) that catalyses one of the final steps in the biosynthesis of γ- and α-tocopherols, which are the main forms of VTE. By reverse genetic approaches, expression analyses, siRNA profiling and DNA methylation assays, we demonstrate that mQTL9-2-6 is an expression QTL associated with differential methylation of a SINE retrotransposon located in the promoter region of VTE3(1). Promoter DNA methylation can be spontaneously reverted leading to different epialleles affecting VTE3(1) expression and VTE content in fruits. These findings indicate therefore that naturally occurring epialleles are responsible for regulation of a nutritionally important metabolic QTL and provide direct evidence of a role for epigenetics in the determination of agronomic traits.L.Q. was recipient of a fellowship of Agencia Nacional de Promoción Científica y Tecnológica and Consejo Nacional de Investigaciones Científicas y Técnicas in Argentina and supported by a postdoctral fellowship from Investissements d’Avenir ANR-10-LABX-54 MEMO LIFE in France. J.A. and L.B. were recipients of a fellowship of Fundação à Amparo da Pesquisa do Estado de São Paulo (Brazil). J.V.C.d.S. was recipient of a fellowship of Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brazil). R.A., L.B. and F.C. are members of Consejo Nacional de Investigaciones Científicas y Técnicas (Argentina). This work was carried out in compliance with current laws governing genetic experimentation in Brazil and in Argentina. This work was supported with grants from Instituto Nacional de Tecnologia Agropecuária, Consejo Nacional de Investigaciones Científicas y Técnicas and Agencia Nacional de Promoción Científica y Tecnológica (Argentina), Fundação à Amparo da Pesquisa do Estado de São Paulo, Conselho Nacional de Desenvolvimento Científico e Tecnológico and Universidade de São Paulo (Brazil); Max Planck Society (Germany); the Agence Nationale de la Recherche (Investissements d’Avenir ANR-10-LABX-54 MEMO LIFE and ANR-11-IDEX-0001-02 PSL* Research University to V.C.); and the European Union (EpiGeneSys FP7 Network of Excellence number 257082 to V.C. and the European Solanaceae Integrated Project FOOD-CT-2006-016214 to F.C., M.R. and A.R.F.)

A communal catalogue reveals Earth's multiscale microbial diversity

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.Peer reviewe

A communal catalogue reveals Earth’s multiscale microbial diversity

Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function.

Reduced glomerular filtration rate defines chronic kidney disease and is associated with cardiovascular and all-cause mortality. We conducted a meta-analysis of genome-wide association studies for estimated glomerular filtration rate (eGFR), combining data across 133,413 individuals with replication in up to 42,166 individuals. We identify 24 new and confirm 29 previously identified loci. Of these 53 loci, 19 associate with eGFR among individuals with diabetes. Using bioinformatics, we show that identified genes at eGFR loci are enriched for expression in kidney tissues and in pathways relevant for kidney development and transmembrane transporter activity, kidney structure, and regulation of glucose metabolism. Chromatin state mapping and DNase I hypersensitivity analyses across adult tissues demonstrate preferential mapping of associated variants to regulatory regions in kidney but not extra-renal tissues. These findings suggest that genetic determinants of eGFR are mediated largely through direct effects within the kidney and highlight important cell types and biological pathways

Determination of Volatile Organic Compounds in Andean Tomato Landraces by Headspace Solid Phase Microextraction-Gas Chromatography-Mass Spectrometry

Traditional tomatoes (Solanum lycopersicum L.) have been mainly selected for their fruit quality and maintained by local farmers in Andean areas of Cuyo and Northwestern Argentina. Volatile organic compounds (VOCs) in mature fruits of Andean tomato landraces were evaluated for the first time using headspace solid phase microextraction (HS-SPME) and gas chromatography-mass spectrometry (GC-MS) and combined with classical multivariate analysis. The data sets composed of 101 volatile metabolites were identi&#64257;ed in 4 accessions of Andean landraces, one commercial variety and one wild tomato accession (Solanum pimpinellifolium L.). The metabolic profile showed typical VOCs of tomato and 21 new compounds never informed in S. lycopersicum. Andean traditional tomatoes have been shown to be metabolically different from wild species. In addition, some varieties of Andean tomatoes have a different profile of VOCs and are richer than the commercial variety. A different and original metabolic volatile composition found in fruits of Andean tomato landraces of Argentina, in comparison with commercial cultivars, might probably reveals selection based on quality attributes made by local farmers

Distribution and Climatic Adaptation of Wild Tomato (Solanum lycopersicum L.) Populations in Mexico

Tomato (Solanum lycopersicum L.) is a vegetable with worldwide importance. Its wild or close related species are reservoirs of genes with potential use for the generation of varieties tolerant or resistant to specific biotic and abiotic factors. The objective was to determine the geographic distribution, ecological descriptors, and patterns of diversity and adaptation of 1296 accessions of native tomato from Mexico. An environmental information system was created with 21 climatic variables with a 1 km2 spatial resolution. Using multivariate techniques (Principal Component Analysis, PCA; Cluster Analysis, CA) and Geographic Information Systems (GIS), the most relevant variables for accession distribution were identified, as well as the groups formed according to the environmental similarity among these. PCA determined that with the first three PCs (Principal Components), it is possible to explain 84.1% of the total variation. The most relevant information corresponded to seasonal variables of temperature and precipitation. CA revealed five statistically significant clusters. Ecological descriptors were determined and described by classifying accessions in Physiographic Provinces. Temperate climates were the most frequent among tomato accessions. Finally, the potential distribution was determined with the Maxent model with 10 replicates by cross-validation, identifying areas with a high probability of tomato presence. These results constitute a reliable source of useful information for planning accession sites collection and identifying accessions that are vulnerable or susceptible to conservation programs