Relationship of weather types on the seasonal and spatial variability of rainfall, runoff, and sediment yield in the western Mediterranean basin
Peña-Angulo, D. ; Nadal-Romero, E. ; González-Hidalgo, J.C. ; Albaladejo, J. ; Andreu, V. ; Barhi, H. ; Bernal, S. ; Biddoccu, M. ; Bienes, R. ; Campo, J. ; Campo-Bescós, M.A. ; Canatário-Duarte, A. ; Cantón, Y. ; Casali, J. ; Castillo, V. ; Cavallo, E. ; Cerdà, A. ; Cid, P. ; Cortesi, N. ; Desir, G. ; Díaz-Pereira, E. ; Espigares, T. ; Estrany, J. ; Farguell, J. ; Fernández-Raga, M. ; Ferreira, C.S. ; Ferro, V. ; Gallart, F. ; Giménez, R. ; Gimeno, E. ; Gómez, J.A. ; Gómez-Gutiérrez, A. ; Gómez-Macpherson, H. ; González-Pelayo, O. ; Kairis, O. ; Karatzas, G.P. ; Keesstra, S. ; Klotz, S. ; Kosmas, C. ; Lana-Renault, N. ; Lasanta, T. ; Latron, J. ; Lázaro, R. ; Bissonnais, Y. Le; Bouteiller, C. Le; Licciardello, F. ; López-Tarazón, J.A. ; Lucía, A. ; Marín-Moreno, V.M. ; Marín, C. ; Marqués, M.J. ; Martínez-Fernández, J. ; Martínez-Mena, M. ; Mateos, L. ; Mathys, N. ; Merino-Martín, L. ; Moreno-de las Heras, M. ; Moustakas, N. ; Nicolau, J.M. ; Pampalone, V. ; Raclot, D. ; Rodríguez-Blanco, M.L. ; Rodrigo-Comino, J. ; Romero-Díaz, A. ; Ruiz-Sinoga, J.D. ; Rubio, J.L. ; Schnabel, S. ; Senciales-González, J.M. ; Solé-Benet, A. ; Taguas, E.V. ; Taboada-Castro, M.T. ; Taboada-Castro, M.M. ; Todisco, F. ; Úbeda, X. ; Varouchakis, E.A. ; Wittenberg, L. ; Zabaleta, A. ; Zorn, M. - \ 2020
Atmosphere 11 (2020)6. - ISSN 2073-4433
Erosion - Mediterraneanbasin - Rainfall - Runoff - Seasonal analyses - Sediment yield - Weather types
Rainfall is the key factor to understand soil erosion processes, mechanisms, and rates. Most research was conducted to determine rainfall characteristics and their relationship with soil erosion (erosivity) but there is little information about how atmospheric patterns control soil losses, and this is important to enable sustainable environmental planning and risk prevention. We investigated the temporal and spatial variability of the relationships of rainfall, runoff, and sediment yield with atmospheric patterns (weather types, WTs) in the western Mediterranean basin. For this purpose, we analyzed a large database of rainfall events collected between 1985 and 2015 in 46 experimental plots and catchments with the aim to: (i) evaluate seasonal differences in the contribution of rainfall, runoff, and sediment yield produced by the WTs; and (ii) to analyze the seasonal efficiency of the different WTs (relation frequency and magnitude) related to rainfall, runoff, and sediment yield. The results indicate two different temporal patterns: the first weather type exhibits (during the cold period: autumn and winter) westerly flows that produce the highest rainfall, runoff, and sediment yield values throughout the territory; the second weather type exhibits easterly flows that predominate during the warm period (spring and summer) and it is located on the Mediterranean coast of the Iberian Peninsula. However, the cyclonic situations present high frequency throughout the whole year with a large influence extended around the western Mediterranean basin. Contrary, the anticyclonic situations, despite of its high frequency, do not contribute significantly to the total rainfall, runoff, and sediment (showing the lowest efficiency) because of atmospheric stability that currently characterize this atmospheric pattern. Our approach helps to better understand the relationship of WTs on the seasonal and spatial variability of rainfall, runoff and sediment yield with a regional scale based on the large dataset and number of soil erosion experimental stations.
Improving the chromatographic selectivity of β-lactam residue analysis in milk using phenyl-column chemistry prior to detection by tandem mass spectrometry
Rocco, Melissa Di; Moloney, Mary ; Haren, Deirdre ; Gutierrez, Montserrat ; Earley, Seán ; Berendsen, Bjorn ; Furey, Ambrose ; Danaher, Martin - \ 2020
Analytical and Bioanalytical Chemistry 412 (2020). - ISSN 1618-2642 - p. 4461 - 4475.
Bovine milk - Chromatographic selectivity - Phenyl-hexyl - UHPLC-MS/MS - β-Lactam antibiotics
Analyte isobaric interferences can limit the development of a comprehensive analytical method for the quantitative liquid chromatography-tandem mass spectrometry profiling of an important cohort of veterinary drugs. In this work, a selective chromatographic separation was developed for the analysis of 32 β-lactam antibiotic residues (12 penicillins, 14 cephalosporins, five carbapenems and faropenem) in milk samples. A range of analytical columns with different stationary phases and mobile phases were evaluated for retention and separation of the β-lactam compounds. Results showed that, among the columns tested, only phenyl-hexyl could adequately separate ampicillin from cephalexin and amoxicillin from cefadroxil, which had shown isobaric interferences on a number of stationary phases. Chromatography was performed using a water/acetonitrile binary gradient with formic acid and ammonium acetate. The β-lactam residues were extracted from the milk samples using a water:acetonitrile solution and purified by C18 dispersive solid-phase extraction (d-SPE) clean-up, followed by concentration under nitrogen and ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) determination. Analytes were monitored in positive electrospray ionisation mode (ESI(+)). Possible interfering matrix effects were overcome by using 13 internal standards. The method was fully validated according to 2002/657/EC guidelines, showing satisfactory performance characteristics. Under within-laboratory reproducibility conditions, trueness and precision ranged from 91 to 130% and from 1.4 to 38.6%, respectively. Decision limits (CCα) were in the range 2.1–133 μg kg−1. Limits of detection (LODs) and quantitation (LOQs) ranged between 0.0090 and 1.5 μg kg−1 and from 0.030 to 5.0 μg kg−1, respectively.
Reproducible molecular networking of untargeted mass spectrometry data using GNPS
Aron, Allegra T. ; Gentry, Emily C. ; McPhail, Kerry L. ; Nothias, Louis Félix ; Nothias-Esposito, Mélissa ; Bouslimani, Amina ; Petras, Daniel ; Gauglitz, Julia M. ; Sikora, Nicole ; Vargas, Fernando ; Hooft, Justin J.J. van der; Ernst, Madeleine ; Kang, Kyo Bin ; Aceves, Christine M. ; Caraballo-Rodríguez, Andrés Mauricio ; Koester, Irina ; Weldon, Kelly C. ; Bertrand, Samuel ; Roullier, Catherine ; Sun, Kunyang ; Tehan, Richard M. ; Boya P, Cristopher A. ; Christian, Martin H. ; Gutiérrez, Marcelino ; Ulloa, Aldo Moreno ; Tejeda Mora, Javier Andres ; Mojica-Flores, Randy ; Lakey-Beitia, Johant ; Vásquez-Chaves, Victor ; Zhang, Yilue ; Calderón, Angela I. ; Tayler, Nicole ; Keyzers, Robert A. ; Tugizimana, Fidele ; Ndlovu, Nombuso ; Aksenov, Alexander A. ; Jarmusch, Alan K. ; Schmid, Robin ; Truman, Andrew W. ; Bandeira, Nuno ; Wang, Mingxun ; Dorrestein, Pieter C. - \ 2020
Nature protocols 15 (2020). - ISSN 1754-2189 - p. 1954 - 1991.
Global Natural Product Social Molecular Networking (GNPS) is an interactive online small molecule–focused tandem mass spectrometry (MS2) data curation and analysis infrastructure. It is intended to provide as much chemical insight as possible into an untargeted MS2 dataset and to connect this chemical insight to the user’s underlying biological questions. This can be performed within one liquid chromatography (LC)-MS2 experiment or at the repository scale. GNPS-MassIVE is a public data repository for untargeted MS2 data with sample information (metadata) and annotated MS2 spectra. These publicly accessible data can be annotated and updated with the GNPS infrastructure keeping a continuous record of all changes. This knowledge is disseminated across all public data; it is a living dataset. Molecular networking—one of the main analysis tools used within the GNPS platform—creates a structured data table that reflects the molecular diversity captured in tandem mass spectrometry experiments by computing the relationships of the MS2 spectra as spectral similarity. This protocol provides step-by-step instructions for creating reproducible, high-quality molecular networks. For training purposes, the reader is led through a 90- to 120-min procedure that starts by recalling an example public dataset and its sample information and proceeds to creating and interpreting a molecular network. Each data analysis job can be shared or cloned to disseminate the knowledge gained, thus propagating information that can lead to the discovery of molecules, metabolic pathways, and ecosystem/community interactions.
A global database of soil nematode abundance and functional group composition
Hoogen, Johan van den; Geisen, Stefan ; Wall, Diana H. ; Wardle, David A. ; Traunspurger, Walter ; Goede, Ron G.M. de; Adams, Byron J. ; Ahmad, Wasim ; Ferris, Howard ; Bardgett, Richard D. ; Bonkowski, Michael ; Campos-Herrera, Raquel ; Cares, Juvenil E. ; Caruso, Tancredi ; Brito Caixeta, Larissa de; Chen, Xiaoyun ; Costa, Sofia R. ; Creamer, Rachel ; Cunha e Castro, José Mauro da; Dam, Marie ; Djigal, Djibril ; Escuer, Miguel ; Griffiths, Bryan S. ; Gutiérrez, Carmen ; Hohberg, Karin ; Kalinkina, Daria ; Kardol, Paul ; Kergunteuil, Alan ; Korthals, Gerard ; Krashevska, Valentyna ; Kudrin, Alexey A. ; Li, Qi ; Liang, Wenju ; Magilton, Matthew ; Marais, Mariette ; Martín, José Antonio Rodríguez ; Matveeva, Elizaveta ; Mayad, El Hassan ; Mzough, E. ; Mulder, Christian ; Mullin, Peter ; Neilson, Roy ; Nguyen, Duong T.A. ; Nielsen, Uffe N. ; Okada, Hiroaki ; Rius, Juan Emilio Palomares ; Pan, Kaiwen ; Peneva, Vlada ; Pellissier, Loïc ; Silva, Julio Carlos Pereira da; Pitteloud, Camille ; Powers, Thomas O. ; Powers, Kirsten ; Quist, Casper W. ; Rasmann, Sergio ; Moreno, Sara Sánchez ; Scheu, Stefan ; Setälä, Heikki ; Sushchuk, Anna ; Tiunov, Alexei V. ; Trap, Jean ; Vestergård, Mette ; Villenave, Cecile ; Waeyenberge, Lieven ; Wilschut, Rutger A. ; Wright, Daniel G. ; Keith, Aidan M. ; Yang, Jiuein ; Schmidt, Olaf ; Bouharroud, R. ; Ferji, Z. ; Putten, Wim H. van der; Routh, Devin ; Crowther, Thomas W. - \ 2020
Scientific Data 7 (2020)1. - ISSN 2052-4463
As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into the spatial distribution patterns of soil nematode abundance and community composition, and the environmental drivers shaping these patterns.
Post-weaning diarrhoea is associated with protein fermentation, alterations in intestinal microbiota, and host physiological parameters in piglets
Hee, B. van der; Gilbert, M.S. ; Kies, Arie ; Fernandez Gutierrez, M.M. ; Vries, H.J.A. de; Taverne, N. ; Taverne-Thiele, J.J. ; Heikamp-de Jong, G.A.M. ; Gaal, Merlijn van; Gerrits, W.J.J. ; Smidt, H. ; Wells, J.M. - \ 2020
In: WIAS Annual Conference 2020. - WIAS - p. 29 - 29.
In Dutch farming, piglets are commonly weaned abruptly around 28 days of age. This abrupt separation from the sow is often associated with a check in feed intake, intestinal morphological changes, and/or aberrations in microbiota composition and activity. Furthermore, the ability to digest solid feed is often underdeveloped, and due to the sudden shift in dietary source often leads to decreased digestion of dietary components, such as protein, in the small intestine. This ultimately leads to a higher flow of undigested nutrients into the colon. In the colon, the long residence time and limited nutrient absorption facilitate microbial proteolysis and accumulation of metabolic end products some of which may be detrimental to the host. Results of our on-farm studies have shown a strong negative correlation between ammonia concentration and dry matter content of the faeces, indicating that diarrhoea is associated with increased ammonia. Furthermore, profiling of the microbial composition revealed an increase in the relative abundance of bacterial groups known for their protein fermenting capacity, and absolute concentrations of genes encoding for specific diarrhoeic toxins, in animals suffering from diarrhoea. To model direct intestinal responses, we assessed molecular mechanisms in our two-dimensional organoid model using protein fermentation metabolites ammonia and hydrogen sulphide, each eliciting distinct cellular responses. From this, we conclude that there are associations between protein fermentation and intestinal health in piglets post-weaning.
In-depth cultivation and characterisation of the pig tonsil microbiome: towards targeted approaches for microbiome manipulation
Fernandes de Oliveira, Isabela ; Fernandez Gutierrez, M.M. ; Baarlen, P. van; Wells, J.M. - \ 2020
In: WIAS Annual Conference 2020. - WIAS - p. 24 - 24.
A salivary metabolite signature that reflects gingival host-microbe interactions: instability predicts gingivitis susceptibility
Fernandez-Gutierrez, Marcela M. ; Imangaliyev, Sultan ; Prodan, Andrei ; Loos, Bruno G. ; Keijser, Bart J.F. ; Kleerebezem, Michiel - \ 2020
Scientific Reports 10 (2020)1. - ISSN 2045-2322
Several proteins and peptides in saliva were shown to stimulate gingival wound repair, but the role of salivary metabolites in this process remains unexplored. In vitro gingival re-epithelialization kinetics were determined using unstimulated saliva samples from healthy individuals collected during an experimental gingivitis study. Elastic net regression with stability selection identified a specific metabolite signature in a training dataset that was associated with the observed re-epithelialization kinetics and enabled its prediction for all saliva samples obtained in the clinical study. This signature encompassed ten metabolites, including plasmalogens, diacylglycerol and amino acid derivatives, which reflect enhanced host-microbe interactions. This association is in agreement with the positive correlation of the metabolite signature with the individual’s gingival bleeding index. Remarkably, intra-individual signature-variation over time was associated with elevated risk for gingivitis development. Unravelling how these metabolites stimulate wound repair could provide novel avenues towards therapeutic approaches in patients with impaired wound healing capacity.
Assessing heavy metal pollution by biomonitoring honeybee nectar in Córdoba (Spain)
Gutiérrez, Miriam ; Molero, Rafael ; Gaju, Miquel ; Steen, Josef van der; Porrini, Claudio ; Ruiz, José Antonio - \ 2020
Environmental Science and Pollution Research 27 (2020). - ISSN 0944-1344 - p. 10436 - 10448.
Bioindication - Biomonitoring - Heavy metals - Honeybee - Nectar - Pollution
Nectar of honeybee colonies has been used in order to identify heavy metals and establish the benefit of this type of studies as a tool for environmental management. For these goals, samples of nectar were obtained from Apis mellifera hives placed in the city of Córdoba (Spain) and its surroundings. Five stations (each with two hives) were selected and samples were collected from May to July of 2007, 2009 and 2010. Concentrations of Pb, Cr, Ni and Cd in nectar were determined by graphite furnace atomic absorption spectrophotometry. Substantial spatial and temporal differences were detected and compared with the values found in bee bodies in a previously published study based on samples obtained simultaneously with those presented in this work. Upper reference thresholds established for this investigation were surpassed frequently by the measures obtained, being Cr (21.43% of samples), stations S3 (22.22%) and S4 (11.12%) year 2009 (22.22%) and the month of July (23.68%) the metal, the locations and the periods that exceeded more times these references. Regarding the Cd, which was studied only in 2010, 33.33% of the nectar samples exceeded the upper reference thresholds. Comparing the biomonitoring of bee bodies and nectar, some coincidences were found, although they showed different results for highest worrisome values of metal, station and year. This suggests that both methods can give complementary information in the surveillance systems of atmospheric pollution.
Similar factors underlie tree abundance in forests in native and alien ranges
Sande, Masha T. van der; Bruelheide, Helge ; Dawson, Wayne ; Dengler, Jürgen ; Essl, Franz ; Field, Richard ; Haider, Sylvia ; Kleunen, Mark van; Kreft, Holger ; Pagel, Joern ; Pergl, Jan ; Purschke, Oliver ; Pyšek, Petr ; Weigelt, Patrick ; Winter, Marten ; Attorre, Fabio ; Aubin, Isabelle ; Bergmeier, Erwin ; Chytrý, Milan ; Dainese, Matteo ; Sanctis, Michele De; Fagundez, Jaime ; Golub, Valentin ; Guerin, Greg R. ; Gutiérrez, Alvaro G. ; Jandt, Ute ; Jansen, Florian ; Jiménez-Alfaro, Borja ; Kattge, Jens ; Kearsley, Elizabeth ; Klotz, Stefan ; Kramer, Koen ; Moretti, Marco ; Niinemets, Ülo ; Peet, Robert K. ; Penuelas, Josep ; Petřík, Petr ; Reich, Peter B. ; Sandel, Brody ; Schmidt, Marco ; Sibikova, Maria ; Violle, Cyrille ; Whitfeld, Timothy J.S. ; Wohlgemuth, Thomas ; Knight, Tiffany M. - \ 2020
Global Ecology and Biogeography 29 (2020)2. - ISSN 1466-822X - p. 281 - 294.
abundance - dissimilarity - forest - functional traits - global - plant invasion - trees
Aim: Alien plant species can cause severe ecological and economic problems, and therefore attract a lot of research interest in biogeography and related fields. To identify potential future invasive species, we need to better understand the mechanisms underlying the abundances of invasive tree species in their new ranges, and whether these mechanisms differ between their native and alien ranges. Here, we test two hypotheses: that greater relative abundance is promoted by (a) functional difference from locally co-occurring trees, and (b) higher values than locally co-occurring trees for traits linked to competitive ability. Location: Global. Time period: Recent. Major taxa studied: Trees. Methods: We combined three global plant databases: sPlot vegetation-plot database, TRY plant trait database and Global Naturalized Alien Flora (GloNAF) database. We used a hierarchical Bayesian linear regression model to assess the factors associated with variation in local abundance, and how these relationships vary between native and alien ranges and depend on species’ traits. Results: In both ranges, species reach highest abundance if they are functionally similar to co-occurring species, yet are taller and have higher seed mass and wood density than co-occurring species. Main conclusions: Our results suggest that light limitation leads to strong environmental and biotic filtering, and that it is advantageous to be taller and have denser wood. The striking similarities in abundance between native and alien ranges imply that information from tree species’ native ranges can be used to predict in which habitats introduced species may become dominant.
Soil eutrophication shaped the composition of pollinator assemblages during the past century
Carvalheiro, Luísa G. ; Biesmeijer, Jacobus C. ; Franzén, Markus ; Aguirre-Gutiérrez, Jesús ; Garibaldi, Lucas A. ; Helm, Aveliina ; Michez, Denis ; Pöyry, Juha ; Reemer, Menno ; Schweiger, Oliver ; Leon van den, Berg ; WallisDeVries, Michiel F. ; Kunin, William E. - \ 2020
Ecography 43 (2020)2. - ISSN 0906-7590 - p. 209 - 221.
extinction debt - herbivory - historical biodiversity changes - nitrogen deposition - nitrophily - pollinator communities
Atmospheric nitrogen deposition and other sources of environmental eutrophication have increased substantially over the past century worldwide, notwithstanding the recent declining trends in Europe. Despite the recognized susceptibility of plants to eutrophication, few studies evaluated how impacts propagate to consumers, such as pollinators. Here we aim to test if soil eutrophication contributes to the temporal dynamics of pollinators and their larval resources. We used a temporally and spatially explicit historical dataset with information on species occurrences to test if soil eutrophication, and more specifically nitrogen deposition, contributes to the patterns of change of plant and pollinator richness in the Netherlands over an 80 yr period. We focus on bees and butterflies, two groups for which we have good knowledge of larval resources that allowed us to define groups of species with different nitrogen related diet preferences. For each group we estimated richness changes between different 20-yr periods at local, regional and national scale, using analytical methods developed for analyzing richness changes based on collection data. Our findings suggest that the impacts of soil eutrophication on plant communities propagate to higher trophic levels, but with a time-lag. Pollinators with nitrogen-related diet preferences were particularly affected, in turn potentially impairing the performance of pollinator-dependent plants. Pollinator declines continued even after their focal plants started to recover. In addition, our results suggest that current levels of nitrogen deposition still have a negative impact on most groups here analyzed, constraining richness recoveries and accentuating declines. Our results indicate that the global increase in nitrogen availability plays an important role in the ongoing pollinator decline. Consequently, species tolerances to soil nitrogen levels should be considered across all trophic levels in management plans that aim to halt biodiversity loss and enhance ecosystems services worldwide.
Molecular characterization of Ecuadorian quinoa (Chenopodium quinoa Willd.) diversity : implications for conservation and breeding
Salazar, Juan ; Jaramillo Roman, Viviana ; Gutierrez, Bernardo ; Loo, E.N. van; Lourdes Torres, María de; Torres, Andrés Francisco - \ 2019
Euphytica 215 (2019)3. - ISSN 0014-2336
Breeding - Ecuador - Genetic diversity - Population structure - Quinoa - SSR
Quinoa (Chenopodium quinoa Willd.) is recognized as an important crop to improve global food security. It has gained international recognition because of the nutritional value of its seeds and its broad agronomic resilience. Although several studies have attempted to characterize the genetic diversity of quinoa, none have focused on evaluating germplasm from Ecuador; the latter considered a relevant subcenter of diversity for the species. In this study, 84 accessions representing the species’ cultivated range in the Ecuadorian Andes were characterized using 15 species-specific SSR markers. The extent of allelic richness (196 alleles) and genetic heterozygosity (H E = 0.71) detected for these accessions demonstrate that Ecuadorian quinoa is highly diverse. Phenetic analyzes structured Ecuadorian germplasm into 3 subgroups; each containing genotypes from all surveyed provinces. Average expected heterozygosity was high for all 3 subgroups (0.53 ≤ H E ≤ 0.72), and Nei-pairwise comparisons showed significant genetic divergence among them (0.31 ≤ Nei DST ≤ 0.84). The lack of a clear geographic pattern in the genetic structure of Ecuadorian quinoa led us to believe that the 3 reported subgroups constitute independent genetic lineages representing ancestral landrace populations which have been disseminated throughout Ecuador via informal seed networks. Nevertheless, a Wilcoxon test showed that at least one subgroup had been subject to intensive inbreeding and selection; and possibly corresponds to the local commercial variety INIAP-Tunkahuan. Our results show that ancestral quinoa diversity in Ecuador has prevailed despite the introduction of commercial varieties, and should be preserved for future use in breeding programs.
Correction to: Molecular characterization of Ecuadorian quinoa (Chenopodium quinoa Willd.) diversity: implications for conservation and breeding
Salazar, Juan ; Roman, Viviana Jaramillo ; Gutierrez, Bernardo ; Loo, Eibertus Nicolaas van; Lourdes Torres, María de; Torres, Andrés Francisco - \ 2019
Euphytica 215 (2019)12. - ISSN 0014-2336
Due to an unfortunate error of miscommunication, two of the co-authors of this manuscript were omitted from the original publication. The correct representation of the authors and their affiliations are listed here and should be treated as definitive. Juan Salazar1, Viviana Jaramillo Roman2, Bernardo Gutierrez1,3, Eibertus Nicolaas van Loo2, Mari´a de Lourdes Torres1, Andre´s Francisco Torres1,2 1. Laboratorio de Biotecnologi´a Vegetal, Colegio de Ciencias Biolo´gicas y Ambientales, Universidad San Francisco de Quito USFQ, Diego de Robles y Vi´a Interocea´nica, Cumbaya´, Ecuador 2. Wageningen UR Plant Breeding, Wageningen University and Research, PO Box 386, 6700 AJ Wageningen, The Netherlands 3. Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK Furthermore, the acknowledgments section has been adapted to match the changes in authorship. The corrected acknowledgements, presented below, are definitive: This research was funded with a Chancellor’s Grant (2015) from Universidad San Francisco de Quito USFQ (Quito-Ecuador). Germplasm access and research permit were granted by the Ministry of Environment of Ecuador (MAE-DNB-CM-2016- 0044). The authors would like to acknowledge the technical assistance offered by researchers at the Plant Biotechnology Laboratory (COCIBA, USFQ), as well as Dr. Leonardo Zurita for his assistance with georeferenced mapping. The authors would also like to acknowledge Dr. Gerard van der Linden (Wageningen University and Research) for supporting our efforts to search and collect quinoa germplasm throughout the Andes of Ecuador.
Global distribution of earthworm diversity
Phillips, Helen R.P. ; Guerra, Carlos A. ; Bartz, Marie L.C. ; Briones, Maria J.I. ; Brown, George ; Crowther, Thomas W. ; Ferlian, Olga ; Gongalsky, Konstantin B. ; Hoogen, Johan Van Den; Krebs, Julia ; Orgiazzi, Alberto ; Routh, Devin ; Schwarz, Benjamin ; Bach, Elizabeth M. ; Bennett, Joanne ; Brose, Ulrich ; Decaëns, Thibaud ; König-Ries, Birgitta ; Loreau, Michel ; Mathieu, Jérôme ; Mulder, Christian ; Putten, Wim H. Van Der; Ramirez, Kelly S. ; Rillig, Matthias C. ; Russell, David ; Rutgers, Michiel ; Thakur, Madhav P. ; Vries, Franciska T. De; Wall, Diana H. ; Wardle, David A. ; Arai, Miwa ; Ayuke, Fredrick O. ; Baker, Geoff H. ; Beauséjour, Robin ; Bedano, José C. ; Birkhofer, Klaus ; Blanchart, Eric ; Blossey, Bernd ; Bolger, Thomas ; Bradley, Robert L. ; Callaham, Mac A. ; Capowiez, Yvan ; Caulfield, Mark E. ; Choi, Amy ; Crotty, Felicity V. ; Dávalos, Andrea ; Diaz Cosin, Darío J. ; Dominguez, Anahí ; Duhour, Andrés Esteban ; Eekeren, Nick Van; Emmerling, Christoph ; Falco, Liliana B. ; Fernández, Rosa ; Fonte, Steven J. ; Fragoso, Carlos ; Franco, André L.C. ; Fugère, Martine ; Fusilero, Abegail T. ; Gholami, Shaieste ; Gundale, Michael J. ; Gutiérrez Lopez, Monica ; Hackenberger, Davorka K. ; Hernández, Luis M. ; Hishi, Takuo ; Holdsworth, Andrew R. ; Holmstrup, Martin ; Hopfensperger, Kristine N. ; Lwanga, Esperanza Huerta ; Huhta, Veikko ; Hurisso, Tunsisa T. ; Iannone, Basil V. ; Iordache, Madalina ; Joschko, Monika ; Kaneko, Nobuhiro ; Kanianska, Radoslava ; Keith, Aidan M. ; Kelly, Courtland A. ; Kernecker, Maria L. ; Klaminder, Jonatan ; Koné, Armand W. ; Kooch, Yahya ; Kukkonen, Sanna T. ; Lalthanzara, H. ; Lammel, Daniel R. ; Lebedev, Iurii M. ; Li, Yiqing ; Jesus Lidon, Juan B. ; Lincoln, Noa K. ; Loss, Scott R. ; Marichal, Raphael ; Matula, Radim ; Moos, Jan Hendrik ; Moreno, Gerardo ; Mor n-Ríos, Alejandro ; Muys, Bart ; Neirynck, Johan ; Norgrove, Lindsey ; Novo, Marta ; Nuutinen, Visa ; Nuzzo, Victoria ; Mujeeb Rahman, P. ; Pansu, Johan ; Paudel, Shishir ; Pérès, Guénola ; Pérez-Camacho, Lorenzo ; Piñeiro, Raúl ; Ponge, Jean François ; Rashid, Muhammad Imtiaz ; Rebollo, Salvador ; Rodeiro-Iglesias, Javier ; Rodríguez, Miguel ; Roth, Alexander M. ; Rousseau, Guillaume X. ; Rozen, Anna ; Sayad, Ehsan ; Schaik, Loes Van; Scharenbroch, Bryant C. ; Schirrmann, Michael ; Schmidt, Olaf ; Schröder, Boris ; Seeber, Julia ; Shashkov, Maxim P. ; Singh, Jaswinder ; Smith, Sandy M. ; Steinwandter, Michael ; Talavera, José A. ; Trigo, Dolores ; Tsukamoto, Jiro ; Valença, Anne W. De; Vanek, Steven J. ; Virto, Iñigo ; Wackett, Adrian A. ; Warren, Matthew W. ; Wehr, Nathaniel H. ; Whalen, Joann K. ; Wironen, Michael B. ; Wolters, Volkmar ; Zenkova, Irina V. ; Zhang, Weixin ; Cameron, Erin K. ; Eisenhauer, Nico - \ 2019
Science 366 (2019)6464. - ISSN 0036-8075 - p. 480 - 485.
Soil organisms, including earthworms, are a key component of terrestrial ecosystems. However, little is known about their diversity, their distribution, and the threats affecting them. We compiled a global dataset of sampled earthworm communities from 6928 sites in 57 countries as a basis for predicting patterns in earthworm diversity, abundance, and biomass. We found that local species richness and abundance typically peaked at higher latitudes, displaying patterns opposite to those observed in aboveground organisms. However, high species dissimilarity across tropical locations may cause diversity across the entirety of the tropics to be higher than elsewhere. Climate variables were found to be more important in shaping earthworm communities than soil properties or habitat cover. These findings suggest that climate change may have serious implications for earthworm communities and for the functions they provide.
Corrigendum: Sialyllactose and Galactooligosaccharides Promote Epithelial Barrier Functioning and Distinctly Modulate Microbiota Composition and Short Chain Fatty Acid Production In Vitro
Perdijk, Olaf ; Baarlen, Peter van; Fernandez-Gutierrez, Marcela M. ; Brink, Erik van den; Schuren, Frank H.J. ; Brugman, Sylvia ; Savelkoul, Huub F.J. ; Kleerebezem, Michiel ; Neerven, R.J.J. van - \ 2019
Frontiers in Immunology 10 (2019). - ISSN 1664-3224 - 1 p.
epithelium - galactooligosaccharides - microbiota - short chain fatty acids - sialyllactose
[This corrects the article DOI: 10.3389/fimmu.2019.00094.].
sPlot – A new tool for global vegetation analyses
Bruelheide, Helge ; Dengler, Jürgen ; Jiménez-Alfaro, Borja ; Purschke, Oliver ; Hennekens, Stephan M. ; Chytrý, Milan ; Pillar, Valério D. ; Jansen, Florian ; Kattge, Jens ; Sandel, Brody ; Aubin, Isabelle ; Biurrun, Idoia ; Field, Richard ; Haider, Sylvia ; Jandt, Ute ; Lenoir, Jonathan ; Peet, Robert K. ; Peyre, Gwendolyn ; Sabatini, Francesco Maria ; Schmidt, Marco ; Schrodt, Franziska ; Winter, Marten ; Aćić, Svetlana ; Agrillo, Emiliano ; Alvarez, Miguel ; Ambarlı, Didem ; Angelini, Pierangela ; Apostolova, Iva ; Arfin Khan, Mohammed A.S. ; Arnst, Elise ; Attorre, Fabio ; Baraloto, Christopher ; Beckmann, Michael ; Berg, Christian ; Bergeron, Yves ; Bergmeier, Erwin ; Bjorkman, Anne D. ; Bondareva, Viktoria ; Borchardt, Peter ; Botta-Dukát, Zoltán ; Boyle, Brad ; Breen, Amy ; Brisse, Henry ; Byun, Chaeho ; Cabido, Marcelo R. ; Casella, Laura ; Cayuela, Luis ; Černý, Tomáš ; Chepinoga, Victor ; Csiky, János ; Curran, Michael ; Ćušterevska, Renata ; Dajić Stevanović, Zora ; Bie, Els De; Ruffray, Patrice de; Sanctis, Michele De; Dimopoulos, Panayotis ; Dressler, Stefan ; Ejrnæs, Rasmus ; El-Sheikh, Mohamed A.E.R.M. ; Enquist, Brian ; Ewald, Jörg ; Fagúndez, Jaime ; Finckh, Manfred ; Font, Xavier ; Forey, Estelle ; Fotiadis, Georgios ; García-Mijangos, Itziar ; Gasper, André Luis de; Golub, Valentin ; Gutierrez, Alvaro G. ; Hatim, Mohamed Z. ; He, Tianhua ; Higuchi, Pedro ; Holubová, Dana ; Hölzel, Norbert ; Homeier, Jürgen ; Indreica, Adrian ; Işık Gürsoy, Deniz ; Jansen, Steven ; Janssen, John ; Jedrzejek, Birgit ; Jiroušek, Martin ; Jürgens, Norbert ; Kącki, Zygmunt ; Kavgacı, Ali ; Kearsley, Elizabeth ; Kessler, Michael ; Knollová, Ilona ; Kolomiychuk, Vitaliy ; Korolyuk, Andrey ; Kozhevnikova, Maria ; Kozub, Łukasz ; Krstonošić, Daniel ; Kühl, Hjalmar ; Kühn, Ingolf ; Kuzemko, Anna ; Küzmič, Filip ; Landucci, Flavia ; Lee, Michael T. ; Levesley, Aurora ; Li, Ching Feng ; Liu, Hongyan ; Lopez-Gonzalez, Gabriela ; Lysenko, Tatiana ; Macanović, Armin ; Mahdavi, Parastoo ; Manning, Peter ; Marcenò, Corrado ; Martynenko, Vassiliy ; Mencuccini, Maurizio ; Minden, Vanessa ; Moeslund, Jesper Erenskjold ; Moretti, Marco ; Müller, Jonas V. ; Munzinger, Jérôme ; Niinemets, Ülo ; Nobis, Marcin ; Noroozi, Jalil ; Nowak, Arkadiusz ; Onyshchenko, Viktor ; Overbeck, Gerhard E. ; Ozinga, Wim A. ; Pauchard, Anibal ; Pedashenko, Hristo ; Peñuelas, Josep ; Pérez-Haase, Aaron ; Peterka, Tomáš ; Petřík, Petr ; Phillips, Oliver L. ; Prokhorov, Vadim ; Rašomavičius, Valerijus ; Revermann, Rasmus ; Rodwell, John ; Ruprecht, Eszter ; Rūsiņa, Solvita ; Samimi, Cyrus ; Schaminée, Joop H.J. ; Schmiedel, Ute ; Šibík, Jozef ; Šilc, Urban ; Škvorc, Željko ; Smyth, Anita ; Sop, Tenekwetche ; Sopotlieva, Desislava ; Sparrow, Ben ; Stančić, Zvjezdana ; Svenning, Jens Christian ; Swacha, Grzegorz ; Tang, Zhiyao ; Tsiripidis, Ioannis ; Turtureanu, Pavel Dan ; Uğurlu, Emin ; Uogintas, Domas ; Valachovič, Milan ; Vanselow, Kim André ; Vashenyak, Yulia ; Vassilev, Kiril ; Vélez-Martin, Eduardo ; Venanzoni, Roberto ; Vibrans, Alexander Christian ; Violle, Cyrille ; Virtanen, Risto ; Wehrden, Henrik von; Wagner, Viktoria ; Walker, Donald A. ; Wana, Desalegn ; Weiher, Evan ; Wesche, Karsten ; Whitfeld, Timothy ; Willner, Wolfgang ; Wiser, Susan ; Wohlgemuth, Thomas ; Yamalov, Sergey ; Zizka, Georg ; Zverev, Andrei - \ 2019
Journal of Vegetation Science 30 (2019)2. - ISSN 1100-9233 - p. 161 - 186.
biodiversity - community ecology - ecoinformatics - functional diversity - global scale - macroecology - phylogenetic diversity - plot database - sPlot - taxonomic diversity - vascular plant - vegetation relevé
Aims: Vegetation-plot records provide information on the presence and cover or abundance of plants co-occurring in the same community. Vegetation-plot data are spread across research groups, environmental agencies and biodiversity research centers and, thus, are rarely accessible at continental or global scales. Here we present the sPlot database, which collates vegetation plots worldwide to allow for the exploration of global patterns in taxonomic, functional and phylogenetic diversity at the plant community level. Results: sPlot version 2.1 contains records from 1,121,244 vegetation plots, which comprise 23,586,216 records of plant species and their relative cover or abundance in plots collected worldwide between 1885 and 2015. We complemented the information for each plot by retrieving climate and soil conditions and the biogeographic context (e.g., biomes) from external sources, and by calculating community-weighted means and variances of traits using gap-filled data from the global plant trait database TRY. Moreover, we created a phylogenetic tree for 50,167 out of the 54,519 species identified in the plots. We present the first maps of global patterns of community richness and community-weighted means of key traits. Conclusions: The availability of vegetation plot data in sPlot offers new avenues for vegetation analysis at the global scale.
Sialyllactose and Galactooligosaccharides Promote Epithelial Barrier Functioning and Distinctly Modulate Microbiota Composition and Short Chain Fatty Acid Production In Vitro
Perdijk, Olaf ; Baarlen, Peter Van; Fernandez-Gutierrez, Marcela M. ; Brink, Erik Van Den; Schuren, Frank H.J. ; Brugman, Sylvia ; Savelkoul, Huub F.J. ; Kleerebezem, Michiel ; Neerven, R.J.J. Van - \ 2019
Frontiers in Immunology 10 (2019). - ISSN 1664-3224
Human milk oligosaccharides (HMO) and prebiotic oligosaccharides are proposed to confer several health benefits to the infant. They shape the microbiota, have anti-inflammatory properties, and support epithelial barrier functioning. However, in order to select the best oligosaccharides for inclusion in infant formulas, there is a need to increase our understanding of the specific effects of HMO and prebiotics on the host immune system. Therefore, we investigated the effects of the HMO sialyllactose (SL), and galactooligosaccharides (GOS) on epithelial barrier functioning, microbiota composition, and SCFA production. The effect of GOS and SL on epithelial barrier functioning and microbiota composition was investigated using in vitro models. Epithelial barrier function was investigated by transcriptome analysis of fully polarized Caco-2 cells exposed for 6 h to SL or GOS. In addition, epithelial cell growth, alkaline phosphatase production, and re-epithelization was studied. Further, we investigated the effect of SL and GOS on microbiota composition and SCFA production using in vitro fecal batch cultures. Transcriptome analysis showed that SL and GOS both induced pathways that regulate cell cycle control. This gene-expression profile translated to a phenotype of halted proliferation and included the induction of alkaline phosphatase activity, a marker of epithelial cell differentiation. SL and GOS also promoted re-epithelialization in an in vitro epithelial wound repair assay. SL and GOS did show distinct modulation of microbiota composition, promoting the outgrowth of Bacteroides and bifidobacteria, respectively, which resulted in distinct changes in SCFA production profiles. Our results show that SL and GOS can both modulate epithelial barrier function by inducing differentiation and epithelial wound repair, but differentially promote the growth of specific genera in the microbiota, which is associated with differential changes in SCFA profiles
Current knowledge and future research opportunities for modeling annual crop mixtures. A review
Gaudio, Noémie ; Escobar-Gutiérrez, Abraham J. ; Casadebaig, Pierre ; Evers, Jochem B. ; Gérard, Frédéric ; Louarn, Gaëtan ; Colbach, Nathalie ; Munz, Sebastian ; Launay, Marie ; Marrou, Hélène ; Barillot, Romain ; Hinsinger, Philippe ; Bergez, Jacques Eric ; Combes, Didier ; Durand, Jean Louis ; Frak, Ela ; Pagès, Loïc ; Pradal, Christophe ; Saint-Jean, Sébastien ; Werf, Wopke van der; Justes, Eric - \ 2019
Agronomy for Sustainable Development 39 (2019)2. - ISSN 1774-0746
Annual crop mixtures - Crop models - Functional–structural plant models - Genotypes mixtures - Individual-based models - Intercrops - Model users
Growing mixtures of annual arable crop species or genotypes is a promising way to improve crop production without increasing agricultural inputs. To design optimal crop mixtures, choices of species, genotypes, sowing proportion, plant arrangement, and sowing date need to be made but field experiments alone are not sufficient to explore such a large range of factors. Crop modeling allows to study, understand, and ultimately design cropping systems and is an established method for sole crops. Recently, modeling started to be applied to annual crop mixtures as well. Here, we review to what extent crop simulation models and individual-based models are suitable to capture and predict the specificities of annual crop mixtures. We argued that (1) the crop mixture spatio-temporal heterogeneity (influencing the occurrence of ecological processes) determines the choice of the modeling approach (plant or crop centered). (2) Only few crop models (adapted from sole crop models) and individual-based models currently exist to simulate annual crop mixtures. Crop models are mainly used to address issues related to both crop mixtures management and the integration of crop mixtures into larger scales such as the rotation. In contrast, individual-based models are mainly used to identify plant traits involved in crop mixture performance and to quantify the relative contribution of the different ecological processes (niche complementarity, facilitation, competition, plasticity) to crop mixture functioning. This review highlights that modeling of annual crop mixtures is in its infancy and gives to model users some important keys to choose the model based on the questions they want to answer, with awareness of the strengths and weaknesses of each of the modeling approaches.
Seminal plasma amino acid profile in different breeds of chicken : Role of seminal plasma on sperm cryoresistance
Santiago-Moreno, Julián ; Bernal, Berenice ; Pérez-Cerezales, Serafín ; Castaño, Cristina ; Toledano-Díaz, Adolfo ; Esteso, Milagros C. ; Gutiérrez-Adán, Alfonso ; López-Sebastián, Antonio ; Gil, María G. ; Woelders, Henri ; Blesbois, Elisabeth - \ 2019
PLoS ONE 14 (2019)1. - ISSN 1932-6203
Seminal plasma is a key biological fluid that modulates sperm function in the reproduction process. However, its role in sperm biotechnologies is scarce in poultry. The aims of the present study were to study the amino acids profile and total proteins of seminal plasma in 12 Spanish chicken breeds and to investigate the role of seminal plasma on cryoresistance of rooster sperm. To investigate the role of seminal plasma on cryoresistance, diluted pooled semen samples were cryopreserved in the presence and absence of seminal plasma. Glutamic acid was the most abundant free amino acid in seminal plasma, followed by alanine, serine, valine, and glycine. There was an influence of breed (P<0.05) on the percentage of viable sperm after freezing-thawing of samples with seminal plasma. Cluster analysis revealed that White Prat, Black Castellana, Blue Andaluza, Quail Castellana, and Red-Barred Vasca returned the best freezing-thawing response (good freezers). There was a positive correlation between seminal plasma concentrations of valine, isoleucine lysine, leucine and post thaw viability. The evaluation of fertilization capacity of frozen-thawed semen from the breeds White Prat (‘good freezer’) and Black-Red Andaluza (‘bad freezer’) showed that good freezer had higher fertility (20/68, 29.4%) compared to bad freezer breed (14/76, 18.4%), even if the difference was not significant (P = 0.08). The TUNEL assay revealed that freezing/thawing procedures in presence of seminal plasma provoked higher DNA fragmentation in most of the breeds, with a positive correlation between seminal alanine, valine, isoleucine, methionine, leucine, tyrosine, phenylalanine concentrations and DNA integrity. DNA fragmentation was lower in absence of seminal plasma and the breed effect on sperm viability was highly reduced. It is concluded that specific seminal plasma amino acids were associated with post-thaw percentage of viable sperm and DNA integrity. The removal of seminal plasma decreases the variability of the results and DNA fragmentation damages.
Global trait–environment relationships of plant communities
Bruelheide, Helge ; Dengler, Jürgen ; Purschke, Oliver ; Lenoir, Jonathan ; Jiménez-Alfaro, Borja ; Hennekens, Stephan M. ; Botta-Dukát, Zoltán ; Chytrý, Milan ; Field, Richard ; Jansen, Florian ; Kattge, Jens ; Pillar, Valério D. ; Schrodt, Franziska ; Mahecha, Miguel D. ; Peet, Robert K. ; Sandel, Brody ; Bodegom, Peter van; Altman, Jan ; Alvarez-Dávila, Esteban ; Arfin Khan, Mohammed A.S. ; Attorre, Fabio ; Aubin, Isabelle ; Baraloto, Christopher ; Barroso, Jorcely G. ; Bauters, Marijn ; Bergmeier, Erwin ; Biurrun, Idoia ; Bjorkman, Anne D. ; Blonder, Benjamin ; Čarni, Andraž ; Cayuela, Luis ; Černý, Tomáš ; Cornelissen, J.H.C. ; Craven, Dylan ; Dainese, Matteo ; Derroire, Géraldine ; Sanctis, Michele De; Díaz, Sandra ; Doležal, Jiří ; Farfan-Rios, William ; Feldpausch, Ted R. ; Fenton, Nicole J. ; Garnier, Eric ; Guerin, Greg R. ; Gutiérrez, Alvaro G. ; Haider, Sylvia ; Hattab, Tarek ; Henry, Greg ; Hérault, Bruno ; Ozinga, Wim A. - \ 2018
Nature Ecology & Evolution 2 (2018)12. - ISSN 2397-334X - p. 1906 - 1917.
Plant functional traits directly affect ecosystem functions. At the species level, trait combinations depend on trade-offs representing different ecological strategies, but at the community level trait combinations are expected to be decoupled from these trade-offs because different strategies can facilitate co-existence within communities. A key question is to what extent community-level trait composition is globally filtered and how well it is related to global versus local environmental drivers. Here, we perform a global, plot-level analysis of trait–environment relationships, using a database with more than 1.1 million vegetation plots and 26,632 plant species with trait information. Although we found a strong filtering of 17 functional traits, similar climate and soil conditions support communities differing greatly in mean trait values. The two main community trait axes that capture half of the global trait variation (plant stature and resource acquisitiveness) reflect the trade-offs at the species level but are weakly associated with climate and soil conditions at the global scale. Similarly, within-plot trait variation does not vary systematically with macro-environment. Our results indicate that, at fine spatial grain, macro-environmental drivers are much less important for functional trait composition than has been assumed from floristic analyses restricted to co-occurrence in large grid cells. Instead, trait combinations seem to be predominantly filtered by local-scale factors such as disturbance, fine-scale soil conditions, niche partitioning and biotic interactions.
Diaporthe diversity and pathogenicity revealed from a broad survey of grapevine diseases in europe
Guarnaccia, V. ; Groenewald, J.Z. ; Woodhall, J. ; Armengol, J. ; Cinelli, T. ; Eichmeier, A. ; Ezra, D. ; Fontaine, F. ; Gramaje, D. ; Gutierrez-Aguirregabiria, A. ; Kaliterna, J. ; Kiss, L. ; Larignon, P. ; Luque, J. ; Mugnai, L. ; Naor, V. ; Raposo, R. ; Sándor, E. ; Váczy, K.Z. ; Crous, P.W. - \ 2018
Persoonia 40 (2018). - ISSN 0031-5850 - p. 135 - 153.
Canker - Multi-locus sequence typing - Pathogenicity - Vitis
Species of Diaporthe are considered important plant pathogens, saprobes, and endophytes on a wide range of plant hosts. Several species are well-known on grapevines, either as agents of pre-or post-harvest infections, including Phomopsis cane and leaf spot, cane bleaching, swelling arm and trunk cankers. In this study we explore the occurrence, diversity and pathogenicity of Diaporthe spp. associated with Vitis vinifera in major grape production areas of Europe and Israel, focusing on nurseries and vineyards. Surveys were conducted in Croatia, Czech Republic, France, Hungary, Israel, Italy, Spain and the UK. A total of 175 Diaporthe strains were isolated from asymptomatic and symptomatic shoots, branches and trunks. A multi-locus phylogeny was established based on five genomic loci (ITS, tef1, cal, his3 and tub2), and the morphological characters of the isolates were determined. Preliminary pathogenicity tests were performed on green grapevine shoots with representative isolates. The most commonly isolated species were D. eres and D. ampelina. Four new Diaporthe species described here as D. bohemiae, D. celeris, D. hispaniae and D. hungariae were found associated with affected vines. Pathogenicity tests revealed D. baccae, D. celeris, D. hispaniae and D. hungariae as pathogens of grapevines. No symptoms were caused by D. bohemiae. This study represents the first report of D. ambigua and D. baccae on grapevines in Europe. The present study improves our understanding of the species associated with several disease symptoms on V. vinifera plants, and provides useful information for effective disease management.