Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Genetic variation in the feeding behavior of isofemale lines of nesidiocoris tenuis
    Chinchilla-Ramírez, Milena ; Pérez-Hedo, Meritxell ; Pannebakker, Bart A. ; Urbaneja, Alberto - \ 2020
    Insects 11 (2020)8. - ISSN 2075-4450 - p. 1 - 13.
    Biological control - Miridae - Phytophagy - Tomato - Zoophagy - Zoophytophagous predator

    Zoophytophagous predators provide biocontrol services in various major crops of modern horticulture due to the combination of its predatory capacity and the induction of plant defenses derived from its phytophagy. However, under certain conditions of prey scarcity, these natural enemies can inflict plant damage. Exploitation of genetic variation and subsequent selective breeding on foraging traits is a potential alternative to overcome this inconvenience. In this study, we quantified the genetic variation of phytophagy and zoophagy of Nesidiocoris tenuis (Reuter) (Hemiptera: Miridae), a zoophytophagous predator widely used in tomato crops to suppress key pests. We compared nine isofemale lines on their capacity to produce necrotic rings and wilting on tomato plants as a proxy for phytophagy, as well as their efficacy to prey on Ephestia kuehniella Zeller (Lepidoptera: Pyralidae) eggs, as a proxy for zoophagy. Differences between isofemale lines in phytophagy and zoophagy indicated a genetic basis. Variation found in the zoophagy levels was larger than that in phytophagy levels. Our results showed that there is a genetic basis for the variation observed in the feeding behavior of isofemale lines of N. tenuis, highlighting the potential importance of selective breeding for such traits of biocontrol interest.

    Global root traits (GRooT) database
    Guerrero-Ramírez, Nathaly R. ; Mommer, Liesje ; Freschet, Grégoire T. ; Iversen, Colleen M. ; McCormack, M.L. ; Kattge, Jens ; Poorter, Hendrik ; Plas, Fons van der; Bergmann, Joana ; Kuyper, Thom W. ; York, Larry M. ; Bruelheide, Helge ; Laughlin, Daniel C. ; Meier, Ina C. ; Roumet, Catherine ; Semchenko, Marina ; Sweeney, Christopher J. ; Ruijven, Jasper van; Valverde-Barrantes, Oscar J. ; Aubin, Isabelle ; Catford, Jane A. ; Manning, Peter ; Martin, Adam ; Milla, Rubén ; Minden, Vanessa ; Pausas, Juli G. ; Smith, Stuart W. ; Soudzilovskaia, Nadejda A. ; Ammer, Christian ; Butterfield, Bradley ; Craine, Joseph ; Cornelissen, Johannes H.C. ; Vries, Franciska T. de; Isaac, Marney E. ; Kramer, Koen ; König, Christian ; Lamb, Eric G. ; Onipchenko, Vladimir G. ; Peñuelas, Josep ; Reich, Peter B. ; Rillig, Matthias C. ; Sack, Lawren ; Shipley, Bill ; Tedersoo, Leho ; Valladares, Fernando ; Bodegom, Peter van; Weigelt, Patrick ; Wright, Justin P. ; Weigelt, Alexandra - \ 2020
    Global Ecology and Biogeography (2020). - ISSN 1466-822X
    Belowground ecology - functional biogeography - macroecological studies - plant form and function - publicly-available database - root traits

    Motivation: Trait data are fundamental to the quantitative description of plant form and function. Although root traits capture key dimensions related to plant responses to changing environmental conditions and effects on ecosystem processes, they have rarely been included in large-scale comparative studies and global models. For instance, root traits remain absent from nearly all studies that define the global spectrum of plant form and function. Thus, to overcome conceptual and methodological roadblocks preventing a widespread integration of root trait data into large-scale analyses we created the Global Root Trait (GRooT) Database. GRooT provides ready-to-use data by combining the expertise of root ecologists with data mobilization and curation. Specifically, we (a) determined a set of core root traits relevant to the description of plant form and function based on an assessment by experts, (b) maximized species coverage through data standardization within and among traits, and (c) implemented data quality checks. Main types of variables contained: GRooT contains 114,222 trait records on 38 continuous root traits. Spatial location and grain: Global coverage with data from arid, continental, polar, temperate and tropical biomes. Data on root traits were derived from experimental studies and field studies. Time period and grain: Data were recorded between 1911 and 2019. Major taxa and level of measurement: GRooT includes root trait data for which taxonomic information is available. Trait records vary in their taxonomic resolution, with subspecies or varieties being the highest and genera the lowest taxonomic resolution available. It contains information for 184 subspecies or varieties, 6,214 species, 1,967 genera and 254 families. Owing to variation in data sources, trait records in the database include both individual observations and mean values. Software format: GRooT includes two csv files. A GitHub repository contains the csv files and a script in R to query the database.

    Plant feeding by Nesidiocoris tenuis : Quantifying its behavioral and mechanical components
    Chinchilla-Ramírez, Milena ; Garzo, Elisa ; Fereres, Alberto ; Gavara-Vidal, Jorge ; Broeke, Cindy J.M. ten; Loon, Joop J.A. van; Urbaneja, Alberto ; Pérez-Hedo, Meritxell - \ 2020
    Biological Control 152 (2020). - ISSN 1049-9644
    Electrical penetration graph - Feeding behavior - Hemiptera - Miridae - Stylectomy - Tomato - Zoophytophagous

    Zoophytophagous predators play an important, though sometimes controversial, role in pest management programs in different crops. In tomato crops, damage caused by phytophagy of the mirid Nesidiocoris tenuis has mainly been reported at high predator population levels or when prey is scarce. Previous research has focused on predator/prey ratios, stylet morphology and saliva composition to explain plant damage by N. tenuis. In this study, we investigated the behavioral and mechanical components of the damage. For this, we compared the feeding behaviors of males, females and fifth-instar nymphs of N. tenuis. Additionally, we investigated the type of stylet activities performed by each stage while probing in plant tissue, using the electrical penetration graph technique (EPG). Furthermore, stylectomy was performed and plant histology studied with the aim to correlate the feeding activities observed in the EPG recordings with stylet tip positions in specific tissues of the leaf petioles. Behavioral observations during a 30-min period showed that nymphs probed more frequently (38.6 ± 1.5 probes) than males and females (25.3 ± 1.1 and 24.3 ± 1.1 probes, respectively). Similarly, nymphs spent a higher proportion of time (656.0 ± 67.6 s) feeding on tomato apical sections compared to males and females (403.0 ± 48.8 s and 356.0 ± 43.7 s, respectively). The EPG recordings during 5 h indicated that cell-rupturing was the main stylet activity for all insect stages, and that fifth-instar nymphs spent a higher proportion of time on cell-rupturing events compared to adults. The histological studies revealed a trend of N. tenuis for the tissues within the vascular semi-ring. The stylet tips were found both in the vascular bundles and in the parenchyma of the interfascicular region. The findings of this study confirm an important role of fifth-instar nymphs feeding behavior in the damage potential of N. tenuis. Moreover, the increased time spent on cell rupturing behaviour suggests that stylet laceration and enzymatic maceration of the saliva occurring during this event might greatly contribute to the inflicted damage. A comprehensive understanding of the interactions of N. tenuis with the plant, at both the behavioral and mechanical levels, might shed light on new approaches to minimize its damage potential to tomato while maintaining its benefits as biocontrol agent.

    Next-generation biological control: the need for integrating genetics and genomics
    Leung, Kelley ; Ras, Erica ; Ferguson, Kim B. ; Ariëns, Simone ; Babendreier, Dirk ; Bijma, Piter ; Bourtzis, Kostas ; Brodeur, Jacques ; Bruins, Margreet A. ; Centurión, Alejandra ; Chattington, Sophie R. ; Chinchilla-Ramírez, Milena ; Dicke, Marcel ; Fatouros, Nina E. ; González-Cabrera, Joel ; Groot, Thomas V.M. ; Haye, Tim ; Knapp, Markus ; Koskinioti, Panagiota ; Hesran, Sophie Le; Lyrakis, Manolis ; Paspati, Angeliki ; Pérez-Hedo, Meritxell ; Plouvier, Wouter N. ; Schlötterer, Christian ; Stahl, Judith M. ; Thiel, Andra ; Urbaneja, Alberto ; Zande, Louis van de; Verhulst, Eveline C. ; Vet, Louise E.M. ; Visser, Sander ; Werren, John H. ; Xia, Shuwen ; Zwaan, Bas J. ; Magalhães, Sara ; Beukeboom, Leo W. ; Pannebakker, Bart A. - \ 2020
    Biological Reviews (2020). - ISSN 1464-7931
    artificial selection - biological control - genetics - genome assembly - genomics - insect breeding - microbiome - modelling

    Biological control is widely successful at controlling pests, but effective biocontrol agents are now more difficult to import from countries of origin due to more restrictive international trade laws (the Nagoya Protocol). Coupled with increasing demand, the efficacy of existing and new biocontrol agents needs to be improved with genetic and genomic approaches. Although they have been underutilised in the past, application of genetic and genomic techniques is becoming more feasible from both technological and economic perspectives. We review current methods and provide a framework for using them. First, it is necessary to identify which biocontrol trait to select and in what direction. Next, the genes or markers linked to these traits need be determined, including how to implement this information into a selective breeding program. Choosing a trait can be assisted by modelling to account for the proper agro-ecological context, and by knowing which traits have sufficiently high heritability values. We provide guidelines for designing genomic strategies in biocontrol programs, which depend on the organism, budget, and desired objective. Genomic approaches start with genome sequencing and assembly. We provide a guide for deciding the most successful sequencing strategy for biocontrol agents. Gene discovery involves quantitative trait loci analyses, transcriptomic and proteomic studies, and gene editing. Improving biocontrol practices includes marker-assisted selection, genomic selection and microbiome manipulation of biocontrol agents, and monitoring for genetic variation during rearing and post-release. We conclude by identifying the most promising applications of genetic and genomic methods to improve biological control efficacy.

    The global abundance of tree palms
    Muscarella, Robert ; Emilio, Thaise ; Phillips, Oliver L. ; Lewis, Simon L. ; Slik, Ferry ; Baker, William J. ; Couvreur, Thomas L.P. ; Eiserhardt, Wolf L. ; Svenning, Jens Christian ; Affum-Baffoe, Kofi ; Aiba, Shin Ichiro ; Almeida, Everton C. de; Almeida, Samuel S. de; Oliveira, Edmar Almeida de; Álvarez-Dávila, Esteban ; Alves, Luciana F. ; Alvez-Valles, Carlos Mariano ; Carvalho, Fabrício Alvim ; Guarin, Fernando Alzate ; Andrade, Ana ; Aragão, Luis E.O.C. ; Murakami, Alejandro Araujo ; Arroyo, Luzmila ; Ashton, Peter S. ; Corredor, Gerardo A.A. ; Baker, Timothy R. ; Camargo, Plinio Barbosa de; Barlow, Jos ; Bastin, Jean François ; Bengone, Natacha Nssi ; Berenguer, Erika ; Berry, Nicholas ; Blanc, Lilian ; Böhning-Gaese, Katrin ; Bonal, Damien ; Bongers, Frans ; Bradford, Matt ; Brambach, Fabian ; Brearley, Francis Q. ; Brewer, Steven W. ; Camargo, Jose L.C. ; Campbell, David G. ; Castilho, Carolina V. ; Castro, Wendeson ; Catchpole, Damien ; Cerón Martínez, Carlos E. ; Chen, Shengbin ; Chhang, Phourin ; Cho, Percival ; Chutipong, Wanlop ; Clark, Connie ; Collins, Murray ; Comiskey, James A. ; Medina, Massiel Nataly Corrales ; Costa, Flávia R.C. ; Culmsee, Heike ; David-Higuita, Heriberto ; Davidar, Priya ; Aguila-Pasquel, Jhon del; Derroire, Géraldine ; Fiore, Anthony Di; Do, Tran Van; Doucet, Jean Louis ; Dourdain, Aurélie ; Drake, Donald R. ; Ensslin, Andreas ; Erwin, Terry ; Ewango, Corneille E.N. ; Ewers, Robert M. ; Fauset, Sophie ; Feldpausch, Ted R. ; Ferreira, Joice ; Ferreira, Leandro Valle ; Fischer, Markus ; Franklin, Janet ; Fredriksson, Gabriella M. ; Gillespie, Thomas W. ; Gilpin, Martin ; Gonmadje, Christelle ; Gunatilleke, Arachchige Upali Nimal ; Hakeem, Khalid Rehman ; Hall, Jefferson S. ; Hamer, Keith C. ; Harris, David J. ; Harrison, Rhett D. ; Hector, Andrew ; Hemp, Andreas ; Herault, Bruno ; Pizango, Carlos Gabriel Hidalgo ; Honorio Coronado, Eurídice N. ; Hubau, Wannes ; Hussain, Mohammad Shah ; Ibrahim, Faridah Hanum ; Imai, Nobuo ; Joly, Carlos A. ; Joseph, Shijo ; Anitha, K. ; Kartawinata, Kuswata ; Kassi, Justin ; Killeen, Timothy J. ; Kitayama, Kanehiro ; Klitgård, Bente Bang ; Kooyman, Robert ; Labrière, Nicolas ; Larney, Eileen ; Laumonier, Yves ; Laurance, Susan G. ; Laurance, William F. ; Lawes, Michael J. ; Levesley, Aurora ; Lisingo, Janvier ; Lovejoy, Thomas ; Lovett, Jon C. ; Lu, Xinghui ; Lykke, Anne Mette ; Magnusson, William E. ; Mahayani, Ni Putu Diana ; Malhi, Yadvinder ; Mansor, Asyraf ; Peña, Jose Luis Marcelo ; Marimon-Junior, Ben H. ; Marshall, Andrew R. ; Melgaco, Karina ; Bautista, Casimiro Mendoza ; Mihindou, Vianet ; Millet, Jérôme ; Milliken, William ; Mohandass, D. ; Mendoza, Abel Lorenzo Monteagudo ; Mugerwa, Badru ; Nagamasu, Hidetoshi ; Nagy, Laszlo ; Seuaturien, Naret ; Nascimento, Marcelo T. ; Neill, David A. ; Neto, Luiz Menini ; Nilus, Rueben ; Vargas, Mario Percy Núñez ; Nurtjahya, Eddy ; Araújo, R.N.O. de; Onrizal, Onrizal ; Palacios, Walter A. ; Palacios-Ramos, Sonia ; Parren, Marc ; Paudel, Ekananda ; Morandi, Paulo S. ; Pennington, R.T. ; Pickavance, Georgia ; Pipoly, John J. ; Pitman, Nigel C.A. ; Poedjirahajoe, Erny ; Poorter, Lourens ; Poulsen, John R. ; Prasad, P.R.C. ; Prieto, Adriana ; Puyravaud, Jean Philippe ; Qie, Lan ; Quesada, Carlos A. ; Ramírez-Angulo, Hirma ; Razafimahaimodison, Jean Claude ; Reitsma, Jan Meindert ; Requena-Rojas, Edilson J. ; Correa, Zorayda Restrepo ; Rodriguez, Carlos Reynel ; Roopsind, Anand ; Rovero, Francesco ; Rozak, Andes ; Lleras, Agustín Rudas ; Rutishauser, Ervan ; Rutten, Gemma ; Punchi-Manage, Ruwan ; Salomão, Rafael P. ; Sam, Hoang Van; Sarker, Swapan Kumar ; Satdichanh, Manichanh ; Schietti, Juliana ; Schmitt, Christine B. ; Marimon, Beatriz Schwantes ; Senbeta, Feyera ; Nath Sharma, Lila ; Sheil, Douglas ; Sierra, Rodrigo ; Silva-Espejo, Javier E. ; Silveira, Marcos ; Sonké, Bonaventure ; Steininger, Marc K. ; Steinmetz, Robert ; Stévart, Tariq ; Sukumar, Raman ; Sultana, Aisha ; Sunderland, Terry C.H. ; Suresh, Hebbalalu Satyanarayana ; Tang, Jianwei ; Tanner, Edmund ; Steege, Hans ter; Terborgh, John W. ; Theilade, Ida ; Timberlake, Jonathan ; Torres-Lezama, Armando ; Umunay, Peter ; Uriarte, María ; Gamarra, Luis Valenzuela ; Bult, Martin van de; Hout, Peter van der; Martinez, Rodolfo Vasquez ; Vieira, Ima Célia Guimarães ; Vieira, Simone A. ; Vilanova, Emilio ; Cayo, Jeanneth Villalobos ; Wang, Ophelia ; Webb, Campbell O. ; Webb, Edward L. ; White, Lee ; Whitfeld, Timothy J.S. ; Wich, Serge ; Willcock, Simon ; Wiser, Susan K. ; Young, Kenneth R. ; Zakaria, Rahmad ; Zang, Runguo ; Zartman, Charles E. ; Zo-Bi, Irié Casimir ; Balslev, Henrik - \ 2020
    Global Ecology and Biogeography 29 (2020)9. - ISSN 1466-822X - p. 1495 - 1514.
    above-ground biomass - abundance patterns - Arecaceae - local abiotic conditions - Neotropics - pantropical biogeography - tropical rainforest - wood density

    Aim: Palms are an iconic, diverse and often abundant component of tropical ecosystems that provide many ecosystem services. Being monocots, tree palms are evolutionarily, morphologically and physiologically distinct from other trees, and these differences have important consequences for ecosystem services (e.g., carbon sequestration and storage) and in terms of responses to climate change. We quantified global patterns of tree palm relative abundance to help improve understanding of tropical forests and reduce uncertainty about these ecosystems under climate change. Location: Tropical and subtropical moist forests. Time period: Current. Major taxa studied: Palms (Arecaceae). Methods: We assembled a pantropical dataset of 2,548 forest plots (covering 1,191 ha) and quantified tree palm (i.e., ≥10 cm diameter at breast height) abundance relative to co-occurring non-palm trees. We compared the relative abundance of tree palms across biogeographical realms and tested for associations with palaeoclimate stability, current climate, edaphic conditions and metrics of forest structure. Results: On average, the relative abundance of tree palms was more than five times larger between Neotropical locations and other biogeographical realms. Tree palms were absent in most locations outside the Neotropics but present in >80% of Neotropical locations. The relative abundance of tree palms was more strongly associated with local conditions (e.g., higher mean annual precipitation, lower soil fertility, shallower water table and lower plot mean wood density) than metrics of long-term climate stability. Life-form diversity also influenced the patterns; palm assemblages outside the Neotropics comprise many non-tree (e.g., climbing) palms. Finally, we show that tree palms can influence estimates of above-ground biomass, but the magnitude and direction of the effect require additional work. Conclusions: Tree palms are not only quintessentially tropical, but they are also overwhelmingly Neotropical. Future work to understand the contributions of tree palms to biomass estimates and carbon cycling will be particularly crucial in Neotropical forests.

    The montane multifunctional landscape: How stakeholders in a biosphere reserve derive benefits and address trade-offs in ecosystem service supply
    Heinze, Alan ; Bongers, Frans ; Ramírez Marcial, Neptalí ; García Barrios, Luis ; Kuyper, Thomas W. - \ 2020
    Ecosystem Services 44 (2020). - ISSN 2212-0416
    Ecosystem service assessments - Local stakeholders - Multifunctional landscapes - Natural protected areas - Trade-offs

    Ecosystem service (ES) assessments, which make an explicit link between nature and people's well-being, can support the management of natural protected areas that face complex and persistent sustainability challenges. We present a case study of ES supply in a biosphere reserve community in southern Mexico. We aimed to identify stakeholder-relevant ES and to analyse trade-offs between them. After engaging local stakeholders, we conducted a biophysical assessment of ES supply and associations across four different land uses. Closed forests and riparian areas, which occurred in different parts of the landscape, supplied high levels of multiple ES. Furthermore, co-produced farming goods and services that supported local livelihoods and conservation-oriented ecosystem services coincided in these four habitats. Together, these habitats provided a diverse array of ES across the landscape, indicating that stakeholders benefited from a multifunctional landscape. At the same time significant trade-offs were found in the supply of forage cover against most other ES, especially tree-based goods and services. These trade-offs revealed conflicts between agricultural land and neighbouring open forests and riparian areas, as well as opposed service demands among beneficiary groups. To address these trade-offs, stakeholders agreed on enhancing forest benefits in order to support both local livelihoods and conservation goals.

    Caracterización de unidades de producción familiar agropecuarias mesoamericanas
    Reyna-Ramírez, Cristian A. ; Fuentes-Ponce, Mariela H. ; Rossing, Walter A.H. ; López-Ridaura, Santiago - \ 2020
    Agrociencia / Colegio de Postgraduados * Programa de Genetica I R E G E P 54 (2020)2. - ISSN 1405-3195 - p. 259 - 277.
    Dependence - Economic poly-activity - Family system - Multivariate analysis

    Farming policies tend to be homogeneous for an entire sector and encourage the implementation of technological innovations without considering the particular characteristics of smallholder farm systems (SFS). The objective of this study was to characterize the SFSs in the Oaxacan Mixteca, Mexico, and the highlands of Guatemala based on typologies, to know their diversity and to have elements to provide guidelines to generate development alternatives. The typology was constructed with information obtained from workshops, surveys and multivariate methods (PCA, cluster analysis and K-means). The variables that determined the diversity of the SFSs were investment capacity, remittances, type of work and livestock activities. The types of SFS identified in the Oaxacan Mixteca were: 1) farming, 2) dependent on external agricultural labours and low monetary income, 3) dependent on government programs, 4) with high non-agricultural income, and 5) medium external income. In the highlands of Guatemala: 1) semi-commercial farming, 2) commercial agriculture, 3) small subsistence, 4) small diversified income, and 5) semi-commercial agriculture. In the Oaxacan Mixteca region, the SFSs are self-consumption systems, dependent on external income (remittances and government programs), in which the potential for development lies in policies, according to the diversity of types and more efficient production systems. In Guatemala, the characteristics of the SFSs comply with global market chains, which regulate production and commercialization conditions, in which the potential for change lies in generating fairer market conditions and more efficient production systems linked to local non-governmental organizations (NGOs). The information obtained based on the typologies is useful for generating specific policies and programs of differentiated support, according to the types of systems and their context.

    Community-level interactions between plants and soil biota during range expansion
    Koorem, Kadri ; Snoek, Basten L. ; Bloem, Janneke ; Geisen, Stefan ; Kostenko, Olga ; Manrubia, Marta ; Ramirez, Kelly S. ; Weser, Carolin ; Wilschut, Rutger A. ; Putten, Wim H. van der - \ 2020
    Journal of Ecology 108 (2020)5. - ISSN 0022-0477 - p. 1860 - 1873.
    bacteria - climate change - fungi - nematodes - plant–plant interactions - plant–soil interactions

    Plant species that expand their range in response to current climate change will encounter soil communities that may hinder, allow or even facilitate plant performance. It has been shown repeatedly for plant species originating from other continents that these plants are less hampered by soil communities from the new than from the original range. However, information about the interactions between intra-continental range expanders and soil communities is sparse, especially at community level. Here we used a plant–soil feedback experiment approach to examine if the interactions between range expanders and soil communities change during range expansion. We grew communities of range-expanding and native plant species with soil communities originating from the original and new range of range expanders. In these conditioned soils, we determined the composition of fungi and bacteria by high-throughput amplicon sequencing of the ITS region and the 16S rRNA gene respectively. Nematode community composition was determined by microscopy-based morphological identification. Then we tested how these soil communities influence the growth of subsequent communities of range expanders and natives. We found that after the conditioning phase soil bacterial, fungal and nematode communities differed by origin and by conditioning plant communities. Despite differences in bacterial, fungal and nematode communities between original and new range, soil origin did not influence the biomass production of plant communities. Both native and range expanding plant communities produced most above-ground biomass in soils that were conditioned by plant communities distantly related to them. Synthesis. Communities of range-expanding plant species shape specific soil communities in both original and new range soil. Plant–soil interactions of range expanders in communities can be similar to the ones of their closely related native plant species.

    Above- and Below-ground Cascading Effects of Wild Ungulates in Temperate Forests
    Ramirez, Ignacio ; Jansen, Patrick A. ; Ouden, Jan den; Moktan, Laxmi ; Herdoiza, Natalie ; Poorter, Lourens - \ 2020
    Ecosystems (2020). - ISSN 1432-9840
    decomposition - invertebrate - litter - mineralization - regeneration - rodent - soil quality - temperate forest - Ungulate

    Ungulates have become abundant in many temperate forests, shifting tree species composition by browsing and altering soil physical conditions by trampling. Whether these effects cascade down to other trophic levels and ecosystem processes is poorly understood. Here, we assess the paths through which ungulates have cascading effects on other trophic levels (regeneration, litter, invertebrates, rodents and organic matter decomposition). We compared ungulate effects by comparing 15 response variables related to different trophic levels between paired fenced and unfenced plots in twelve temperate forest sites across the Netherlands, and used pathway analysis model to identify the (in)direct pathways through which ungulates have influenced these variables. We found that plots with ungulates (that is, unfenced) compared to plots without (that is, fenced) had lower litter depth, sapling diversity, sapling density, rodent activity, macro-invertebrate biomass, decomposition rate of tea bags, pine and birch litter and higher soil compaction. These findings were used in a path analysis to establish potential causal relationships, which showed that ungulate presence: decreased sapling density, which indirectly decreased rodent activity; decreased litter depth, which indirectly reduced invertebrate diversity; increased soil compaction, which also decreased invertebrate diversity. Soil pH decreased invertebrate biomass, which also increased nitrogen mineralization. Yet, we did not find cascading effects of ungulates on decomposition rates. Importantly, an increase in ungulate abundance strengthens the cascading effects in this system. Our results suggest that ungulates can trigger cascading effects on lower trophic levels, yet decomposition and mineralization rates are resilient to ungulate browsing and trampling. Therefore, temperate forests conservation could benefit by limiting ungulate abundance.

    Dietary patterns are related to cognitive functioning in elderly enriched with individuals at increased risk for Alzheimer’s disease
    Wesselman, L.M.P. ; Lent, Melo van; Schröder, A. ; Rest, O. van de; Peters, O. ; Menne, F. ; Fuentes, M. ; Priller, J. ; Spruth, E.J. ; Altenstein, S. ; Schneider, A. ; Fließbach, K. ; Roeske, S. ; Wolfsgruber, S. ; Kleineidam, L. ; Spottke, A. ; Pross, V. ; Wiltfang, J. ; Vukovich, R. ; Schild, A.K. ; Düzel, E. ; Metzger, C.D. ; Glanz, W. ; Buerger, K. ; Janowitz, D. ; Perneczky, R. ; Tatò, M. ; Teipel, S. ; Kilimann, I. ; Laske, C. ; Buchmann, M. ; Ramirez, A. ; Sikkes, S.A.M. ; Jessen, F. ; Flier, W.M. van der; Wagner, M. - \ 2020
    European Journal of Nutrition (2020). - ISSN 1436-6207
    Cognition - Dementia - Dietary patterns - Mediterranean diet - MIND diet

    Purpose: To investigate cross-sectional associations between dietary patterns and cognitive functioning in elderly free of dementia. Methods: Data of 389 participants from the German DELCODE study (52% female, 69 ± 6 years, mean Mini Mental State Score 29 ± 1) were included. The sample was enriched with elderly at increased risk for Alzheimer’s disease (AD) by including participants with subjective cognitive decline, mild cognitive impairment (MCI) and siblings of AD patients. Mediterranean and MIND diets were derived from 148 Food Frequency Questionnaire items, and data-driven patterns by principal component analysis (PCA) of 39 food groups. Associations between dietary patterns and five cognitive domain scores were analyzed with linear regression analyses adjusted for demographics (model 1), and additionally for energy intake, BMI, other lifestyle variables and APOe4-status (model 2). For PCA-derived dietary components, final model 3 included all other dietary components. Results: In fully adjusted models, adherence to Mediterranean and MIND diet was associated with better memory. The ‘alcoholic beverages’ PCA component was positively associated with most cognitive domains. Exclusion of MCI subjects (n = 60) revealed that Mediterranean and MIND diet were also related to language functions; associations with the alcoholic beverages component were attenuated, but most remained significant. Conclusion: In line with data from elderly population samples, Mediterranean and MIND diet and some data-derived dietary patterns were related to memory and language function. Longitudinal data are needed to draw conclusions on the putative effect of nutrition on the rate of cognitive decline, and on the potential of dietary interventions in groups at increased risk for AD.

    A schematic sampling protocol for contaminant monitoring in raptors
    Espín, Silvia ; Andevski, Jovan ; Duke, Guy ; Eulaers, Igor ; Gómez-Ramírez, Pilar ; Hallgrimsson, Gunnar Thor ; Helander, Björn ; Herzke, Dorte ; Jaspers, Veerle L.B. ; Krone, Oliver ; Lourenço, Rui ; María-Mojica, Pedro ; Martínez-López, Emma ; Mateo, Rafael ; Movalli, Paola ; Sánchez-Virosta, Pablo ; Shore, Richard F. ; Sonne, Christian ; Brink, Nico W. van den; Hattum, Bert van; Vrezec, Al ; Wernham, Chris ; García-Fernández, Antonio J. - \ 2020
    Ambio (2020). - ISSN 0044-7447
    Best practices - Birds of prey - Falcons - Large-scale biomonitoring - Owls - Pan-European network

    Birds of prey, owls and falcons are widely used as sentinel species in raptor biomonitoring programmes. A major current challenge is to facilitate large-scale biomonitoring by coordinating contaminant monitoring activities and by building capacity across countries. This requires sharing, dissemination and adoption of best practices addressed by the Networking Programme Research and Monitoring for and with Raptors in Europe (EURAPMON) and now being advanced by the ongoing international COST Action European Raptor Biomonitoring Facility. The present perspective introduces a schematic sampling protocol for contaminant monitoring in raptors. We provide guidance on sample collection with a view to increasing sampling capacity across countries, ensuring appropriate quality of samples and facilitating harmonization of procedures to maximize the reliability, comparability and interoperability of data. The here presented protocol can be used by professionals and volunteers as a standard guide to ensure harmonised sampling methods for contaminant monitoring in raptors.

    Long-term thermal sensitivity of Earth's tropical forests
    Sullivan, Martin J.P. ; Lewis, Simon L. ; Affum-Baffoe, Kofi ; Castilho, Carolina ; Costa, Flávia ; Sanchez, Aida Cuni ; Ewango, Corneille E.N. ; Hubau, Wannes ; Marimon, Beatriz ; Monteagudo-Mendoza, Abel ; Qie, Lan ; Sonké, Bonaventure ; Martinez, Rodolfo Vasquez ; Baker, Timothy R. ; Brienen, Roel J.W. ; Feldpausch, Ted R. ; Galbraith, David ; Gloor, Manuel ; Malhi, Yadvinder ; Aiba, Shin Ichiro ; Alexiades, Miguel N. ; Almeida, Everton C. ; Oliveira, Edmar Almeida de; Dávila, Esteban Álvarez ; Loayza, Patricia Alvarez ; Andrade, Ana ; Vieira, Simone Aparecida ; Aragão, Luiz E.O.C. ; Araujo-Murakami, Alejandro ; Arets, Eric J.M.M. ; Arroyo, Luzmila ; Ashton, Peter ; Aymard C, Gerardo ; Baccaro, Fabrício B. ; Banin, Lindsay F. ; Baraloto, Christopher ; Camargo, Plínio Barbosa ; Barlow, Jos ; Barroso, Jorcely ; Bastin, Jean François ; Batterman, Sarah A. ; Beeckman, Hans ; Begne, Serge K. ; Bennett, Amy C. ; Berenguer, Erika ; Berry, Nicholas ; Blanc, Lilian ; Boeckx, Pascal ; Bogaert, Jan ; Bonal, Damien ; Bongers, Frans ; Bradford, Matt ; Brearley, Francis Q. ; Brncic, Terry ; Brown, Foster ; Burban, Benoit ; Camargo, José Luís ; Castro, Wendeson ; Céron, Carlos ; Ribeiro, Sabina Cerruto ; Moscoso, Victor Chama ; Chave, Jerôme ; Chezeaux, Eric ; Clark, Connie J. ; Souza, Fernanda Coelho de; Collins, Murray ; Comiskey, James A. ; Valverde, Fernando Cornejo ; Medina, Massiel Corrales ; Costa, Lola da; Dančák, Martin ; Dargie, Greta C. ; Davies, Stuart ; Cardozo, Nallaret Davila ; Haulleville, Thales de; Medeiros, Marcelo Brilhante de; Aguila Pasquel, Jhon Del; Derroire, Géraldine ; Fiore, Anthony Di; Doucet, Jean Louis ; Dourdain, Aurélie ; Droissant, Vincent ; Duque, Luisa Fernanda ; Ekoungoulou, Romeo ; Elias, Fernando ; Erwin, Terry ; Esquivel-Muelbert, Adriane ; Fauset, Sophie ; Ferreira, Joice ; Llampazo, Gerardo Flores ; Foli, Ernest ; Ford, Andrew ; Gilpin, Martin ; Hall, Jefferson S. ; Hamer, Keith C. ; Hamilton, Alan C. ; Harris, David J. ; Hart, Terese B. ; Hédl, Radim ; Herault, Bruno ; Herrera, Rafael ; Higuchi, Niro ; Hladik, Annette ; Coronado, Eurídice Honorio ; Huamantupa-Chuquimaco, Isau ; Huasco, Walter Huaraca ; Jeffery, Kathryn J. ; Jimenez-Rojas, Eliana ; Kalamandeen, Michelle ; Djuikouo, Marie Noël Kamdem ; Kearsley, Elizabeth ; Umetsu, Ricardo Keichi ; Kho, Lip Khoon ; Killeen, Timothy ; Kitayama, Kanehiro ; Klitgaard, Bente ; Koch, Alexander ; Labrière, Nicolas ; Laurance, William ; Laurance, Susan ; Leal, Miguel E. ; Levesley, Aurora ; Lima, Adriano J.N. ; Lisingo, Janvier ; Lopes, Aline P. ; Lopez-Gonzalez, Gabriela ; Lovejoy, Tom ; Lovett, Jon C. ; Lowe, Richard ; Magnusson, William E. ; Malumbres-Olarte, Jagoba ; Manzatto, Ângelo Gilberto ; Marimon, Ben Hur ; Marshall, Andrew R. ; Marthews, Toby ; Almeida Reis, Simone Matias de; Maycock, Colin ; Melgaço, Karina ; Mendoza, Casimiro ; Metali, Faizah ; Mihindou, Vianet ; Milliken, William ; Mitchard, Edward T.A. ; Morandi, Paulo S. ; Mossman, Hannah L. ; Nagy, Laszlo ; Nascimento, Henrique ; Neill, David ; Nilus, Reuben ; Vargas, Percy Núñez ; Palacios, Walter ; Camacho, Nadir Pallqui ; Peacock, Julie ; Pendry, Colin ; Peñuela Mora, Maria Cristina ; Pickavance, Georgia C. ; Pipoly, John ; Pitman, Nigel ; Playfair, Maureen ; Poorter, Lourens ; Poulsen, John R. ; Poulsen, Axel Dalberg ; Preziosi, Richard ; Prieto, Adriana ; Primack, Richard B. ; Ramírez-Angulo, Hirma ; Reitsma, Jan ; Réjou-Méchain, Maxime ; Correa, Zorayda Restrepo ; Sousa, Thaiane Rodrigues de; Bayona, Lily Rodriguez ; Roopsind, Anand ; Rudas, Agustín ; Rutishauser, Ervan ; Abu Salim, Kamariah ; Salomão, Rafael P. ; Schietti, Juliana ; Sheil, Douglas ; Silva, Richarlly C. ; Espejo, Javier Silva ; Valeria, Camila Silva ; Silveira, Marcos ; Simo-Droissart, Murielle ; Simon, Marcelo Fragomeni ; Singh, James ; Soto Shareva, Yahn Carlos ; Stahl, Clement ; Stropp, Juliana ; Sukri, Rahayu ; Sunderland, Terry ; Svátek, Martin ; Swaine, Michael D. ; Swamy, Varun ; Taedoumg, Hermann ; Talbot, Joey ; Taplin, James ; Taylor, David ; Steege, Hans Ter; Terborgh, John ; Thomas, Raquel ; Thomas, Sean C. ; Torres-Lezama, Armando ; Umunay, Peter ; Gamarra, Luis Valenzuela ; Heijden, Geertje van der; Hout, Peter van der; Meer, Peter van der; Nieuwstadt, Mark van; Verbeeck, Hans ; Vernimmen, Ronald ; Vicentini, Alberto ; Vieira, Ima Célia Guimarães ; Torre, Emilio Vilanova ; Vleminckx, Jason ; Vos, Vincent ; Wang, Ophelia ; White, Lee J.T. ; Willcock, Simon ; Woods, John T. ; Wortel, Verginia ; Young, Kenneth ; Zagt, Roderick ; Zemagho, Lise ; Zuidema, Pieter A. ; Zwerts, Joeri A. ; Phillips, Oliver L. - \ 2020
    Science 368 (2020)6493. - ISSN 0036-8075 - p. 869 - 874.

    The sensitivity of tropical forest carbon to climate is a key uncertainty in predicting global climate change. Although short-term drying and warming are known to affect forests, it is unknown if such effects translate into long-term responses. Here, we analyze 590 permanent plots measured across the tropics to derive the equilibrium climate controls on forest carbon. Maximum temperature is the most important predictor of aboveground biomass (-9.1 megagrams of carbon per hectare per degree Celsius), primarily by reducing woody productivity, and has a greater impact per °C in the hottest forests (>32.2°C). Our results nevertheless reveal greater thermal resilience than observations of short-term variation imply. To realize the long-term climate adaptation potential of tropical forests requires both protecting them and stabilizing Earth's climate.

    Enabling reusability of plant phenomic datasets with MIAPPE 1.1
    Papoutsoglou, Evangelia A. ; Faria, Daniel ; Arend, Daniel ; Arnaud, Elizabeth ; Athanasiadis, Ioannis N. ; Chaves, Inês ; Coppens, Frederik ; Cornut, Guillaume ; Costa, Bruno V. ; Ćwiek-Kupczyńska, Hanna ; Droesbeke, Bert ; Finkers, Richard ; Gruden, Kristina ; Junker, Astrid ; King, Graham J. ; Krajewski, Paweł ; Lange, Matthias ; Laporte, Marie Angélique ; Michotey, Célia ; Oppermann, Markus ; Ostler, Richard ; Poorter, Hendrik ; Ramı́rez-Gonzalez, Ricardo ; Ramšak, Živa ; Reif, Jochen C. ; Rocca-Serra, Philippe ; Sansone, Susanna Assunta ; Scholz, Uwe ; Tardieu, François ; Uauy, Cristobal ; Usadel, Björn ; Visser, Richard G.F. ; Weise, Stephan ; Kersey, Paul J. ; Miguel, Célia M. ; Adam-Blondon, Anne Françoise ; Pommier, Cyril - \ 2020
    New Phytologist 227 (2020)1. - ISSN 0028-646X - p. 260 - 273.
    findability - interoperability - metadata - phenomics - plant phenotyping - reusability - standards

    Enabling data reuse and knowledge discovery is increasingly critical in modern science, and requires an effort towards standardising data publication practices. This is particularly challenging in the plant phenotyping domain, due to its complexity and heterogeneity. We have produced the MIAPPE 1.1 release, which enhances the existing MIAPPE standard in coverage, to support perennial plants, in structure, through an explicit data model, and in clarity, through definitions and examples. We evaluated MIAPPE 1.1 by using it to express several heterogeneous phenotyping experiments in a range of different formats, to demonstrate its applicability and the interoperability between the various implementations. Furthermore, the extended coverage is demonstrated by the fact that one of the datasets could not have been described under MIAPPE 1.0. MIAPPE 1.1 marks a major step towards enabling plant phenotyping data reusability, thanks to its extended coverage, and especially the formalisation of its data model, which facilitates its implementation in different formats. Community feedback has been critical to this development, and will be a key part of ensuring adoption of the standard.

    Diet diversity and pesticide risk mediate the negative effects of land use change on solitary bee offspring production
    Centrella, Mary ; Russo, Laura ; Moreno Ramírez, Natalia ; Eitzer, Brian ; Dyke, Maria van; Danforth, Bryan ; Poveda, Katja - \ 2020
    Journal of Applied Ecology 57 (2020)6. - ISSN 0021-8901 - p. 1031 - 1042.
    agroecosystems - bee decline - floral resources - land use change - Osmia cornifrons - pesticide toxicity - pollinator health - solitary bees

    Threats to bee pollinators such as land use change, high pesticide risk and reduced floral diet diversity are usually assessed independently, even though they often co-occur to impact bees in agroecosystems. We established populations of the non-native mason bee Osmia cornifrons at 17 NY apple orchards varying in proportion of surrounding agriculture and measured floral diet diversity and pesticide risk levels in the pollen provisions they produced. We used path analysis to test the direct and indirect effects of different habitats, diet diversity and pesticide risk on emergent female offspring number and weight. High proportions of agricultural habitat surrounding bee nests indirectly reduced the number of female offspring produced, by reducing floral diet diversity in pollen. When the proportion of agriculture surrounding bee nests was high, bees collected increased proportions of Rosaceae in their pollen provisions, which marginally (0.05 < p < 0.1) increased fungicide risk levels in pollen. This, in turn, marginally reduced female offspring weight. In contrast, female offspring weight increased as proportions surrounding open habitat (wildflowers, grassland and pasture) increased, but this effect was not influenced by proportion Rosaceae or fungicide risk levels in pollen. Synthesis and applications. Threats to bee health such as land use change, pesticide exposure and changes in pollen diet composition are often studied in isolation. However, our results suggest that these threats can simultaneously influence one another to impact bee populations in the agroecosystems where we rely on them for pollination. By replacing surrounding agricultural habitats with more natural habitats, such as grasslands and pastures, we can increase floral diet diversity and reduce pesticide exposure in bee-collected pollen, resulting in healthier mason bee populations in apple orchards.

    CGIAR modeling approaches for resource-constrained scenarios : I. Accelerating crop breeding for a changing climate
    Ramirez-Villegas, Julian ; Molero Milan, Anabel ; Alexandrov, Nickolai ; Asseng, Senthold ; Challinor, Andrew J. ; Crossa, Jose ; Eeuwijk, Fred van; Ghanem, Michel Edmond ; Grenier, Cecile ; Heinemann, Alexandre B. ; Wang, Jiankang ; Juliana, Philomin ; Kehel, Zakaria ; Kholova, Jana ; Koo, Jawoo ; Pequeno, Diego ; Quiroz, Roberto ; Rebolledo, Maria C. ; Sukumaran, Sivakumar ; Vadez, Vincent ; White, Jeffrey W. ; Reynolds, Matthew - \ 2020
    Crop Science 60 (2020)2. - ISSN 0011-183X - p. 547 - 567.

    Crop improvement efforts aiming at increasing crop production (quantity, quality) and adapting to climate change have been subject of active research over the past years. But, the question remains ‘to what extent can breeding gains be achieved under a changing climate, at a pace sufficient to usefully contribute to climate adaptation, mitigation and food security?’. Here, we address this question by critically reviewing how model-based approaches can be used to assist breeding activities, with particular focus on all CGIAR (formerly the Consultative Group on International Agricultural Research but now known simply as CGIAR) breeding programs. Crop modeling can underpin breeding efforts in many different ways, including assessing genotypic adaptability and stability, characterizing and identifying target breeding environments, identifying tradeoffs among traits for such environments, and making predictions of the likely breeding value of the genotypes. Crop modeling science within the CGIAR has contributed to all of these. However, much progress remains to be done if modeling is to effectively contribute to more targeted and impactful breeding programs under changing climates. In a period in which CGIAR breeding programs are undergoing a major modernization process, crop modelers will need to be part of crop improvement teams, with a common understanding of breeding pipelines and model capabilities and limitations, and common data standards and protocols, to ensure they follow and deliver according to clearly defined breeding products. This will, in turn, enable more rapid and better-targeted crop modeling activities, thus directly contributing to accelerated and more impactful breeding efforts.

    Cultivation of Bacteria From Aplysina aerophoba: Effects of Oxygen and Nutrient Gradients
    Gutleben, Johanna ; Loureiro, Catarina ; Ramírez Romero, Laura Adriana ; Shetty, Sudarshan ; Wijffels, René H. ; Smidt, Hauke ; Sipkema, Detmer - \ 2020
    Frontiers in Microbiology 11 (2020). - ISSN 1664-302X
    antibiotic resistance - Aplysina aerophoba - environmental microbes - marine sponge - microbial cultivation - viability PCR

    Sponge-associated bacteria possess biotechnologically interesting properties but as yet have largely evaded cultivation. Thus, “omics”-based information on the ecology and functional potential of sponge symbionts is awaiting its integration into the design of innovative cultivation approaches. To cultivate bacteria derived from the marine sponge Aplysina aerophoba, nine novel media formulations were created based on the predicted genomic potential of the prevalent sponge symbiont lineage Poribacteria. In addition, to maintain potential microbial metabolic interactions in vitro, a Liquid-Solid cultivation approach and a Winogradsky-column approach were applied. The vast majority of microorganisms in the inoculum appeared viable after cryopreservation of sponge specimen as determined by selective propidium monoazide DNA modification of membrane-compromised cells, however, only 2% of the initial prokaryotic diversity could be recovered through cultivation. In total, 256 OTUs encompassing seven prokaryotic phyla were cultivated. The diversity of the cultivated community was influenced by the addition of the antibiotic aeroplysinin-1 as well as by medium dilution, rather than carbon source. Furthermore, the Winogradsky-column approach reproducibly enriched distinct communities at different column depths, amongst which were numerous Clostridia and OTUs that could not be assigned to a known phylum. While some bacterial taxa such as Pseudovibrio and Ruegeria were recovered from nearly all applied cultivation conditions, others such as Bacteroidetes were specific to certain medium types. Predominant sponge-associated prokaryotic taxa remained uncultured, nonetheless, alternative cultivation approaches applied here enriched for previously uncultivated microbes.

    Acquiring plant features with optical sensing devices in an organic strip-cropping system
    Krus, Anne ; Apeldoorn, Dirk Van; Valero, Constantino ; Ramirez, Juan José - \ 2020
    Agronomy 10 (2020)2. - ISSN 2073-4395
    Cabbages - Lidar - Plant extraction - Point cloud - Weighted sum

    The SUREVEG project focuses on improvement of biodiversity and soil fertility in organic agriculture through strip-cropping systems. To counter the additional workforce a robotic tool is proposed. Within the project, a modular proof of concept (POC) version will be produced that will combine detection technologies with actuation on a single-plant level in the form of a robotic arm. This article focuses on the detection of crop characteristics through point clouds obtained with two lidars. Segregation in soil and plants was successfully achieved without the use of additional data from other sensor types, by calculating weighted sums, resulting in a dynamically obtained threshold criterion. This method was able to extract the vegetation from the point cloud in strips with varying vegetation coverage and sizes. The resulting vegetation clouds were compared to drone imagery, to prove they perfectly matched all green areas in said image. By dividing the remaining clouds of overlapping plants by means of the nominal planting distance, the number of plants, their volumes, and thereby the expected yields per row could be determined.

    PathBank: a comprehensive pathway database for model organisms
    Wishart, David S. ; Li, Carin ; Marcu, Ana ; Badran, Hasan ; Pon, Allison ; Budinski, Zachary ; Patron, Jonas ; Lipton, Debra ; Cao, Xuan ; Oler, Eponine ; Li, Krissa ; Paccoud, Maïlys ; Hong, Chelsea ; Guo, An C. ; Chan, Christopher ; Wei, William ; Ramirez-Gaona, Miguel - \ 2020
    Nucleic acids research 48 (2020)D1. - ISSN 0305-1048 - p. D470 - D478.

    PathBank (www.pathbank.org) is a new, comprehensive, visually rich pathway database containing more than 110 000 machine-readable pathways found in 10 model organisms (Homo sapiens, Bos taurus, Rattus norvegicus, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, Saccharomyces cerevisiae, Escherichia coli and Pseudomonas aeruginosa). PathBank aims to provide a pathway for every protein and a map for every metabolite. This resource is designed specifically to support pathway elucidation and pathway discovery in transcriptomics, proteomics, metabolomics and systems biology. It provides detailed, fully searchable, hyperlinked diagrams of metabolic, metabolite signaling, protein signaling, disease, drug and physiological pathways. All PathBank pathways include information on the relevant organs, organelles, subcellular compartments, cofactors, molecular locations, chemical structures and protein quaternary structures. Each small molecule is hyperlinked to the rich data contained in public chemical databases such as HMDB or DrugBank and each protein or enzyme complex is hyperlinked to UniProt. All PathBank pathways are accompanied with references and detailed descriptions which provide an overview of the pathway, condition or processes depicted in each diagram. Every PathBank pathway is downloadable in several machine-readable and image formats including BioPAX, SBML, PWML, SBGN, RXN, PNG and SVG. PathBank also supports community annotations and submissions through the web-based PathWhiz pathway illustrator. The vast majority of PathBank's pathways (>95%) are not found in any other public pathway database.

    Towards an integrative understanding of soil biodiversity
    Thakur, Madhav P. ; Phillips, Helen R.P. ; Brose, Ulrich ; Vries, Franciska T. De; Lavelle, Patrick ; Loreau, Michel ; Mathieu, Jerome ; Mulder, Christian ; Putten, Wim H. Van der; Rillig, Matthias C. ; Wardle, David A. ; Bach, Elizabeth M. ; Bartz, Marie L.C. ; Bennett, Joanne M. ; Briones, Maria J.I. ; Brown, George ; Decaëns, Thibaud ; Eisenhauer, Nico ; Ferlian, Olga ; Guerra, Carlos António ; König-Ries, Birgitta ; Orgiazzi, Alberto ; Ramirez, Kelly S. ; Russell, David J. ; Rutgers, Michiel ; Wall, Diana H. ; Cameron, Erin K. - \ 2020
    Biological Reviews 95 (2020)2. - ISSN 1464-7931 - p. 350 - 364.
    alpha diversity - beta diversity - biodiversity theory - metacommunity theory - neutral theory - niche theory - spatial scale - species–energy relationship - theory of island biogeography

    Soil is one of the most biodiverse terrestrial habitats. Yet, we lack an integrative conceptual framework for understanding the patterns and mechanisms driving soil biodiversity. One of the underlying reasons for our poor understanding of soil biodiversity patterns relates to whether key biodiversity theories (historically developed for aboveground and aquatic organisms) are applicable to patterns of soil biodiversity. Here, we present a systematic literature review to investigate whether and how key biodiversity theories (species–energy relationship, theory of island biogeography, metacommunity theory, niche theory and neutral theory) can explain observed patterns of soil biodiversity. We then discuss two spatial compartments nested within soil at which biodiversity theories can be applied to acknowledge the scale-dependent nature of soil biodiversity.

    Techno-economic comparative assessment of novel lignin depolymerization routes to bio-based aromatics
    Vural Gursel, Iris ; Dijkstra, Jan W. ; Huijgen, Wouter J.J. ; Ramirez, Andrea - \ 2019
    Biofuels Bioproducts and Biorefining 13 (2019)4. - ISSN 1932-104X - p. 1068 - 1084.
    biobased aromatics - hydrodeoxygenation - hydrothermal upgrading - lignin depolymerization - lignin valorization - lignocellulosic biorefinery - pyrolysis - techno-economic analysis

    This paper presents a techno-economic assessment of three novel routes for the production of bio-based aromatics from lignin. It aims to provide insights into their feasibility and hotspots at an early stage of development to guide further research and development and to facilitate commercialization. The lignin conversion routes are: (non-catalytic) lignin pyrolysis, direct hydrodeoxygenation (HDO), and hydrothermal upgrading (HyThUp). The products generated are mixed oxygenated aromatic monomers (MOAMON), light organics, heavy organics, and char. For the technical assessment, conceptual design followed by process modeling in Aspen Plus was based on experimental yields. The models generated indispensable data on material and energy flows. An economic assessment was then conducted by estimating operating and capital costs. Return on investment (ROI), payback period (PBP), and net present value (NPV) were used as key performance indicators. Downstream processing was especially demanding in the HyThUp process due to the presence of a significant flow rate of water in the system, which significantly increased external utility requirements. Due to complex separations, the HyThUp process showed the highest capital cost (35% more than pyrolysis). Operating costs were the highest for the direct HDO process (34% more than pyrolysis) due to the use of hydrogen. Overall, the direct HDO process showed the highest ROI (12%) and the shortest PBP (5 years) due to high yields of valuable heavy organics (32%) and MOAMON (24%). Direct HDO was found to be feasible with a positive NPV based on prices used in the assessment. Among the three processes investigated, the direct HDO process therefore appeared to be the most promising, and consideration should be given to further development and commercialization of this process.

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