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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WoSIS: standardised soil profile data for digital soil mapping at global scale
Carvalho Ribeiro, E.D. ; Batjes, N.H. - \ 2019
In: Geophysical Research Abstracts. - EGU (Geophysical Research Abstracts 2018 )
SoilGrids: consistent soil information to assess and map soil functions at global scale
Poggio, Laura ; Duque Moreira de Sousa, Luïs ; Heuvelink, G.B.M. ; Kempen, B. ; Batjes, N.H. ; Leenaars, J.G.B. ; Mantel, S. ; Bai, Z.G. ; Turdukulov, Ulan ; Ruiperez Gonzalez, M. ; Carvalho Ribeiro, E.D. ; Rossiter, David ; Bosch, H. van den - \ 2019
In: Wageningen Soil Conference: Understanding Soil Functions. - Wageningen : ISRIC - p. 50 - 51.
WoSIS snapshot - September 2019
Batjes, Niels ; Carvalho Ribeiro, Eloi ; Oostrum, Ad van - \ 2019
ISRIC
soil - standard - bulk density - cation exchange capacity (CEC) - soil classification - coarse fragments - clay - effective cation exchange capacity (ECEC) - electrical conductivity - organic carbon - pH - sand - silt - calcium carbonate equivalent - texture - water retention - WoSIS - WoSIS snapshot
The World Soil Information Service (WoSIS) provides quality-assessed and standardised soil profile data to support digital soil mapping and environmental applications at broad scale levels. Since the release of the first ‘WoSIS snapshot’, in July 2016, many new soil data were shared with us, registered in the ISRIC data repository, and subsequently standardised in accordance with the licences specified by the data providers. Soil profile data managed in WoSIS were contributed by a wide range of data providers, therefore special attention was paid to measures for soil data quality and the standardisation of soil property definitions, soil property values (and units of measurement), and soil analytical method descriptions. We presently consider the following soil chemical properties (organic carbon, total carbon, total carbonate equivalent, total Nitrogen, Phosphorus (extractable-P, total-P, and P-retention), soil pH, cation exchange capacity, and electrical conductivity) and physical properties (soil texture (sand, silt, and clay), bulk density, coarse fragments, and water retention), grouped according to analytical procedures (aggregates) that are operationally comparable. Further, for each profile, we provide the original soil classification (FAO, WRB, USDA, and version) and horizon designations insofar as these have been specified in the source databases. Measures for geographical accuracy (i.e. location) of the point data as well as a first approximation for the uncertainty associated with the operationally defined analytical methods are presented, for possible consideration in digital soil mapping and subsequent earth system modelling. The present snapshot, referred to as ‘WoSIS snapshot - September 2019’, comprises 196,498 geo-referenced profiles originating from 173 countries. They represent over 832 thousand soil layers (or horizons), and over 6 million records. The actual number of observations for each property varies (greatly) between profiles and with depth, this generally depending on the objectives of the initial soil sampling programmes.
Rarity of monodominance in hyperdiverse Amazonian forests
Steege, Hans Ter; Henkel, Terry W. ; Helal, Nora ; Marimon, Beatriz S. ; Marimon-Junior, Ben Hur ; Huth, Andreas ; Groeneveld, Jürgen ; Sabatier, Daniel ; Souza Coelho, Luiz de; Andrade Lima Filho, Diogenes de; Salomão, Rafael P. ; Amaral, Iêda Leão ; Almeida Matos, Francisca Dionízia de; Castilho, Carolina V. ; Phillips, Oliver L. ; Guevara, Juan Ernesto ; Jesus Veiga Carim, Marcelo de; Cárdenas López, Dairon ; Magnusson, William E. ; Wittmann, Florian ; Irume, Mariana Victória ; Martins, Maria Pires ; Silva Guimarães, José Renan da; Molino, Jean François ; Bánki, Olaf S. ; Piedade, Maria Teresa Fernandez ; Pitman, Nigel C.A. ; Mendoza, Abel Monteagudo ; Ramos, José Ferreira ; Luize, Bruno Garcia ; Moraes de Leão Novo, Evlyn Márcia ; Núñez Vargas, Percy ; Silva, Thiago Sanna Freire ; Venticinque, Eduardo Martins ; Manzatto, Angelo Gilberto ; Reis, Neidiane Farias Costa ; Terborgh, John ; Casula, Katia Regina ; Honorio Coronado, Euridice N. ; Montero, Juan Carlos ; Feldpausch, Ted R. ; Duque, Alvaro ; Costa, Flávia R.C. ; Arboleda, Nicolás Castaño ; Schöngart, Jochen ; Killeen, Timothy J. ; Vasquez, Rodolfo ; Mostacedo, Bonifacio ; Demarchi, Layon O. ; Assis, Rafael L. ; Baraloto, Chris ; Engel, Julien ; Petronelli, Pascal ; Castellanos, Hernán ; Medeiros, Marcelo Brilhante de; Quaresma, Adriano ; Simon, Marcelo Fragomeni ; Andrade, Ana ; Camargo, José Luís ; Laurance, Susan G.W. ; Laurance, William F. ; Rincón, Lorena M. ; Schietti, Juliana ; Sousa, Thaiane R. ; Sousa Farias, Emanuelle de; Lopes, Maria Aparecida ; Magalhães, José Leonardo Lima ; Mendonça Nascimento, Henrique Eduardo ; Lima de Queiroz, Helder ; Aymard C, Gerardo A. ; Brienen, Roel ; Revilla, Juan David Cardenas ; Vieira, Ima Célia Guimarães ; Cintra, Bruno Barçante Ladvocat ; Stevenson, Pablo R. ; Feitosa, Yuri Oliveira ; Duivenvoorden, Joost F. ; Mogollón, Hugo F. ; Araujo-Murakami, Alejandro ; Ferreira, Leandro Valle ; Lozada, José Rafael ; Comiskey, James A. ; Toledo, José Julio de; Damasco, Gabriel ; Dávila, Nállarett ; Draper, Freddie ; García-Villacorta, Roosevelt ; Lopes, Aline ; Vicentini, Alberto ; Alonso, Alfonso ; Dallmeier, Francisco ; Gomes, Vitor H.F. ; Lloyd, Jon ; Neill, David ; Aguiar, Daniel Praia Portela de; Arroyo, Luzmila ; Carvalho, Fernanda Antunes ; Souza, Fernanda Coelho de; Amaral, Dário Dantas do; Feeley, Kenneth J. ; Gribel, Rogerio ; Pansonato, Marcelo Petratti ; Barlow, Jos ; Berenguer, Erika ; Ferreira, Joice ; Fine, Paul V.A. ; Guedes, Marcelino Carneiro ; Jimenez, Eliana M. ; Licona, Juan Carlos ; Peñuela Mora, Maria Cristina ; Villa, Boris ; Cerón, Carlos ; Maas, Paul ; Silveira, Marcos ; Stropp, Juliana ; Thomas, Raquel ; Baker, Tim R. ; Daly, Doug ; Dexter, Kyle G. ; Huamantupa-Chuquimaco, Isau ; Milliken, William ; Pennington, Toby ; Ríos Paredes, Marcos ; Fuentes, Alfredo ; Klitgaard, Bente ; Pena, José Luis Marcelo ; Peres, Carlos A. ; Silman, Miles R. ; Tello, J.S. ; Chave, Jerome ; Cornejo Valverde, Fernando ; Fiore, Anthony Di; Hilário, Renato Richard ; Phillips, Juan Fernando ; Rivas-Torres, Gonzalo ; Andel, Tinde R. van; Hildebrand, Patricio von; Noronha, Janaína Costa ; Barbosa, Edelcilio Marques ; Barbosa, Flávia Rodrigues ; Matos Bonates, Luiz Carlos de; Sá Carpanedo, Rainiellen de; Dávila Doza, Hilda Paulette ; Fonty, Émile ; GómeZárate Z, Ricardo ; Gonzales, Therany ; Gallardo Gonzales, George Pepe ; Hoffman, Bruce ; Junqueira, André Braga ; Malhi, Yadvinder ; Andrade Miranda, Ires Paula de; Pinto, Linder Felipe Mozombite ; Prieto, Adriana ; Jesus Rodrigues, Domingos de; Rudas, Agustín ; Ruschel, Ademir R. ; Silva, Natalino ; Vela, César I.A. ; Vos, Vincent Antoine ; Zent, Egleé L. ; Zent, Stanford ; Weiss Albuquerque, Bianca ; Cano, Angela ; Carrero Márquez, Yrma Andreina ; Correa, Diego F. ; Costa, Janaina Barbosa Pedrosa ; Flores, Bernardo Monteiro ; Galbraith, David ; Holmgren, Milena ; Kalamandeen, Michelle ; Nascimento, Marcelo Trindade ; Oliveira, Alexandre A. ; Ramirez-Angulo, Hirma ; Rocha, Maira ; Scudeller, Veridiana Vizoni ; Sierra, Rodrigo ; Tirado, Milton ; Umaña Medina, Maria Natalia ; Heijden, Geertje van der; Vilanova Torre, Emilio ; Vriesendorp, Corine ; Wang, Ophelia ; Young, Kenneth R. ; Ahuite Reategui, Manuel Augusto ; Baider, Cláudia ; Balslev, Henrik ; Cárdenas, Sasha ; Casas, Luisa Fernanda ; Farfan-Rios, William ; Ferreira, Cid ; Linares-Palomino, Reynaldo ; Mendoza, Casimiro ; Mesones, Italo ; Torres-Lezama, Armando ; Giraldo, Ligia Estela Urrego ; Villarroel, Daniel ; Zagt, Roderick ; Alexiades, Miguel N. ; Oliveira, Edmar Almeida de; Garcia-Cabrera, Karina ; Hernandez, Lionel ; Palacios Cuenca, Walter ; Pansini, Susamar ; Pauletto, Daniela ; Ramirez Arevalo, Freddy ; Sampaio, Adeilza Felipe ; Valderrama Sandoval, Elvis H. ; Valenzuela Gamarra, Luis ; Levesley, Aurora ; Pickavance, Georgia ; Melgaço, Karina - \ 2019
Scientific Reports 9 (2019). - ISSN 2045-2322

Tropical forests are known for their high diversity. Yet, forest patches do occur in the tropics where a single tree species is dominant. Such "monodominant" forests are known from all of the main tropical regions. For Amazonia, we sampled the occurrence of monodominance in a massive, basin-wide database of forest-inventory plots from the Amazon Tree Diversity Network (ATDN). Utilizing a simple defining metric of at least half of the trees ≥ 10 cm diameter belonging to one species, we found only a few occurrences of monodominance in Amazonia, and the phenomenon was not significantly linked to previously hypothesized life history traits such wood density, seed mass, ectomycorrhizal associations, or Rhizobium nodulation. In our analysis, coppicing (the formation of sprouts at the base of the tree or on roots) was the only trait significantly linked to monodominance. While at specific locales coppicing or ectomycorrhizal associations may confer a considerable advantage to a tree species and lead to its monodominance, very few species have these traits. Mining of the ATDN dataset suggests that monodominance is quite rare in Amazonia, and may be linked primarily to edaphic factors.

Applying the aboveground-belowground interaction concept in agriculture: Spatio-temporal scales matter
Veen, G.F. ; Jasper Wubs, E.R. ; Bardgett, Richard D. ; Barrios, Edmundo ; Bradford, Mark A. ; Carvalho, Sabrina ; Deyn, Gerlinde B. De; Vries, Franciska T. de; Giller, Ken E. ; Kleijn, David ; Landis, Douglas A. ; Rossing, Walter A.H. ; Schrama, Maarten ; Six, Johan ; Struik, Paul C. ; Gils, Stijn van; Wiskerke, Johannes S.C. ; Putten, Wim H. van der; Vet, Louise E.M. - \ 2019
Frontiers in Ecology and Evolution 7 (2019)AUG. - ISSN 2296-701X
Above-belowground biotic interactions - Agroecology - Spatio-temporal scales - Steering communities - Sustainable agriculture

Interactions between aboveground and belowground organisms are important drivers of plant growth and performance in natural ecosystems. Making practical use of such above-belowground biotic interactions offers important opportunities for enhancing the sustainability of agriculture, as it could favor crop growth, nutrient supply, and defense against biotic and abiotic stresses. However, the operation of above-and belowground organisms at different spatial and temporal scales provides important challenges for application in agriculture. Aboveground organisms, such as herbivores and pollinators, operate at spatial scales that exceed individual fields and are highly variable in abundance within growing seasons. In contrast, pathogenic, symbiotic, and decomposer soil biota operate at more localized spatial scales from individual plants to patches of square meters, however, they generate legacy effects on plant performance that may last from single to multiple years. The challenge is to promote pollinators and suppress pests at the landscape and field scale, while creating positive legacy effects of local plant-soil interactions for next generations of plants. Here, we explore the possibilities to improve utilization of above-belowground interactions in agro-ecosystems by considering spatio-temporal scales at which aboveground and belowground organisms operate. We identified that successful integration of above-belowground biotic interactions initially requires developing crop rotations and intercropping systems that create positive local soil legacy effects for neighboring as well subsequent crops. These configurations may then be used as building blocks to design landscapes that accommodate beneficial aboveground communities with respect to their required resources. For successful adoption of above-belowground interactions in agriculture there is a need for context-specific solutions, as well as sound socio-economic embedding.

Corrigendum: Exposure to antibiotics affects Saponin immersion-induced immune stimulation and shift in microbial composition in Zebrafish larvae
Nadal, Adrià López ; Peggs, David ; Wiegertjes, Geert F. ; Brugman, Sylvia - \ 2019
Frontiers in Microbiology 10 (2019). - ISSN 1664-302X

In the original article, there was an error. The name of the transgenic line used was incorrect. The correct name of the line is "mpeg1:mCherry/mpx:eGFPi114" Corrections have been made to the Materials and Methods subsection Animals: "Adult Tg(mpeg1:mCherry/mpx:eGFPi114) (Renshaw et al., 2006; Bernut et al., 2014) zebrafish (kindly provided by Prof. Meijer, Leiden University), expressing mCherry under the macrophage-specific mpeg1 promotor and GFP under the neutrophil-specific mpx promotor were housed in Zebtec family tanks (Tecniplast, Buguggiate, Italy) under continuous flow-through at 28°C (14/10-hour light/dark cycle) at Carus facilities (WUR, Wageningen, Netherlands). Zebrafish were fed with a mixture of Artemia 230.000 npg (Ocean Nutrition Europe, Essen, Belgium) and Tetramin Flakes (Tetra, Melle, Germany) twice per day. Embryos were obtained by natural spawning and raised with E3 water (0.10 mM NaCl in demineralized water, pH 7.6) in petri dishes at 28°C (12/12-hour light/dark cycle) (Westerfield, 2007). Dead or fungus-infected embryos were identified by microscopy and discarded in tricaine/E3 solution [8.4% (v/v) 24 mM Tricaine (Sigma-Aldrich, DL, United States) stock solution in E3]. Larval ages are expressed in days post-fertilization (dpf). From 5 dpf onward larvae were fed with live daily cultured Tetrahymena pyriformis." Materials and Methods, subsection Dose-Response Experiment Saponin Exposure: "Double Tg(mpeg1:mCherry /mpx:eGFPi114) zebrafish larvae were randomly distributed in 6 well plates (n = 20 fish/well) and exposed to different concentrations [0, 0.5, 0.7 and 1.0 mg/ml] of saponin [ultrapure Soy Saponin 95%, kindly provided by Trond Kortner NMBU Oslo Norway, origin: Organic Technologies, Coshocton, OH (Krogdahl et al., 2015)] dissolved in the E3 (10 ml solution/well) from 6-9 dpf. Mortality was registered and all media were refreshed daily. At 24 h (7 dpf) and 72 h (9 dpf) after the start of the immersion, zebrafish (n = 6-11/group) were anaesthetized embedded and imaged using fluorescent microscopy (as described below). Per time point several larvae were euthanized for further analysis with an overdose MS-222 (8.4 ml of 24 mM Tricaine (Sigma-Aldrich, DL, United States) in 100 ml E3). Pools of 5 larvae were used for RNA extraction (3 pools per group at 24 h, 7-9 pools per group at 72 h) and gene expression was measured on cDNA by Real Time PCR (as described below). Two independent experiments were performed and data were combined." Materials and Methods, subsection Fluorescent in vivo imaging: "Tg(mpeg1:mCherry/mpx:eGFPi114) zebrafish larvae were anaesthetized with tricaine/E3 solution (4.2 ml of 24 mM Tricaine (Sigma-Aldrich, DL, United States) in 100 ml E3) and embedded in 1% low melting point agarose (Thermo Fisher Scientific, MA, United States). Larvae were imaged as whole mounts with a Leica M205 FA Fluorescence Stereo Microscope. After image acquisition, pictures were analyzed with ImageJ® software (United States National Institutes of Health, Bethesda, United States). The intestinal regions were manually selected per fish on the basis of the bright light picture and subsequently copied to the green and red channel pictures (Supplementary Figure S1). Within this intestinal region individual cells were counted for each fish. Furthermore, corrected total cell fluorescence (CTCF) was measured in ImageJ® on total fish larvae by using the following formula: Integrated density-(area of total fish x mean fluorescence of the background reading)." Material and Methods, subsection Experimental Design and Sampling Strategy Antibiotics and Saponin Exposure: A graphical representation of the experimental design and analysis performed per time-point is displayed in Figure 1. To assess the effect of antibiotics, 4 dpf Tg(mpeg1:mCherry/mpx:eGFPi114) fish were randomly distributed in five 6 well-plates (n = 20 fish/well) and 3 treatment conditions were established: (1) control (E3), (2) ciprofloxacin 5 μg/L (Sigma-Aldrich, DL, United States) or (3) oxytetracycline hydrochloride 5 μg/L (Sigma-Aldrich, DL, United States) (10 ml solution/well). The dose of antibiotics was based on several reviews and experimental papers summarizing environmental concentrations of antibiotics in water environments (Ding and He, 2010; Carvalho and Santos, 2016; Watts et al., 2017; Patrolecco et al., 2018; Zhou et al., 2018b) to be at a low dose (ng-μg/L range) and not acute dose (mg/L range). At 6 dpf, 4 pools of 5 larvae were sampled to assess changes in gene expression at baseline. Moreover, at 6 dpf DNA was isolated from 3 pools of 5 larvae to investigate microbiome composition at baseline. In vivo imaging was performed on n = 10 larvae/group to visualize innate immune cells. Subsequently, after sampling, at 6 dpf ultrapure soy saponin was applied to half of the remaining larvae at a concentration 0.5 mg/ml (to induce mild immune stimulation) so each treatment group was split into two, resulting in 6 treatment groups: (1) control, (2) ciprofloxacin (5 μg/L), (3) oxytetracycline hydrochloride (5 μg/L), (4) saponin (0.5 mg/ml), (5) ciprofloxacin + saponin (5 μg/L + 0.5 mg/ml), and (6) oxytetracycline hydrochloride + saponin (5 μg/L + 0.5 mg/ml). All treatment media were refreshed daily. At 9 dpf in vivo imaging was performed on n = 10 larvae/group to visualize innate immune cells. Gene expression was performed on 4 pools of 5 larvae to investigate immune gene expression and from 3 pools of 5 larvae DNA was isolated for microbiological analysis. Because of the error reported above, corrections have also been made to the Figure legends of Figure 2 and Figure 4. The correct legends appear below. Figure 2: Effect of saponin immersion on zebrafish larvae. (A) Percent survival of zebrafish exposed to control (E3), 0.5 mg/ml saponin, 0.7 mg/ml saponin and 1 mg/ml saponin from 6-9 dpf (n = 40 fish/treatment) (Log-rank Mantel-Cox Test for Chi-square, ∗∗∗p < 0.0005). (B) Representative pictures of the saponin-treated Tg(mpeg1:mCherry/mpx:eGFPi114) fish displaying green neutrophils and red macrophages. (C) Quantification of neutrophils and macrophages in the intestinal area (n = 6-11 fish/group) (one way ANOVA Kruskal-Wallis test with Dunn's Multiple comparison Post-Test, mean ± SEM, ∗p < 0.05 ∗∗p < 0.01). Top: counted cells in intestinal area. Bottom: Corrected Total Cell Fluorescence (CTCF, measure for total fluorescent pixels in the whole fish). Two independent experiments were performed and data are combined. Figure 4: Effect of antibiotic exposure on saponin-immune-stimulation. (A) Percent survival of zebrafish exposed to control (E3), ciprofloxacin (4-9 dpf) (5 ug/L) or oxytetracycline (4-9 dpf) (5 ug/ml) + /- saponin (0.5 mg/ml) from 6-9 dpf (n = 100 fish / treatment) (Log-rank Mantel-Cox Test for Chi-square). (B) Representative pictures of the antibiotic/saponin-treated Tg(mpeg1:mCherry/mpx:eGFPi114) fish displaying green neutrophils and red macrophages. (C) Quantification of neutrophils and macrophages in the intestinal area (n = 10 fish/ group) (one way ANOVA Kruskal-Wallis test with Dunn's Multiple comparison Post-Test, mean ± SEM, ∗p < 0.05). Two independent experiments were performed and one representative experiment is shown. The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated.

Root architecture system of oilseed species from the Jatropha genus during seed development and germination
Brito, Cristiane D. de; Loureiro, Marta B. ; Ribeiro, Paulo R. ; Vasconcelos, Paulo Carvalho T. ; Moreno, Maria Lúcia V. ; Fernandez, Luzimar G. ; Hilhorst, Henk W.M. ; Lammeren, Andre van; Ligterink, Wilco ; Castro, Renato D. de - \ 2019
Industrial Crops and Products 139 (2019). - ISSN 0926-6690
Germination - Guard cells - Root development - Seed embryo

The life cycle of a seed plant involves subsequent stages of development including germination and seedling establishment. Morphological structures have a fundamental role in these phases, since they are strongly related to physiological adaptations to survival in a range of environments. The present study describes an important morphophysiological and anatomical pattern in embryos of Jatropha genus, involving adaptations for germination and seedling growth. Seed embryos of Jatropha curcas, J. gossypiifolia, J. podagrica and J. multifida were examined using different physiological and microscopic assays. Jatropha species present a multimeristematic embryo composed of one main apical primary meristem plus four radial primary meristems. Seed germination is completed by simultaneous protrusion of five functional roots and seedlings are able to survive even with only one of them. The hypocotyl-radicle transition zone exhibiting different stomata sizes, ontogenic phases and short lifespan limited to the germination. Stomata fractures at mid-region due to the fact that guard cells were not lengthen as neighboring epidermal cells, forming a large cavity in the epidermal tissue during seedling growth. The results showed an unusual and complex root structure for the Jatropha genus. The presence of stomata operating strictly during seed germination could be associated to intense energetic metabolism demanded for the simultaneous growth of the five roots originated from the multimeristematic radicle. This study provides important insights into the understanding of seed germination of Jatropha species in response to stress environmental conditions.

Genome-wide association studies for heat stress response in Bos taurus × Bos indicus crossbred cattle
Otto, Pamela I. ; Guimarães, Simone E.F. ; Verardo, Lucas L. ; Azevedo, Ana Luísa S. ; Vandenplas, Jeremie ; Sevillano, Claudia A. ; Marques, Daniele B.D. ; Fatima A. Pires, Maria de; Freitas, Célio de; Verneque, R.S. ; Martins, Marta Fonseca ; Panetto, João Cláudio C. ; Carvalho, Wanessa A. ; Gobo, Diego O.R. ; Silva, Marcos Vinícius G.B. da; Machado, Marco A. - \ 2019
Journal of Dairy Science 102 (2019)9. - ISSN 0022-0302 - p. 8148 - 8158.
crossbred cattle - gene network - heat stress - post-GWAS analyses

Heat stress is an important issue in the global dairy industry. In tropical areas, an alternative to overcome heat stress is the use of crossbred animals or synthetic breeds, such as the Girolando. In this study, we performed a genome-wide association study (GWAS) and post-GWAS analyses for heat stress in an experimental Gir × Holstein F2 population. Rectal temperature (RT) was measured in heat-stressed F2 animals, and the variation between 2 consecutive RT measurements (ΔRT) was used as the dependent variable. Illumina BovineSNP50v1 BeadChip (Illumina Inc., San Diego, CA) and single-SNP approach were used for GWAS. Post-GWAS analyses were performed by gene ontology terms enrichment and gene-transcription factor (TF) networks, generated from enriched TF. The breed origin of marker alleles in the F2 population was assigned using the breed of origin of alleles (BOA) approach. Heritability and repeatability estimates (± standard error) for ΔRT were 0.13 ± 0.08 and 0.29 ± 0.06, respectively. Association analysis revealed 6 SNP significantly associated with ΔRT. Genes involved with biological processes in response to heat stress effects (LIF, OSM, TXNRD2, and DGCR8) were identified as putative candidate genes. After performing the BOA approach, the 10% of F2 animals with the lowest breeding values for ΔRT were classified as low-ΔRT, and the 10% with the highest breeding values for ΔRT were classified as high-ΔRT. On average, 49.4% of low-ΔRT animals had 2 alleles from the Holstein breed (HH), and 39% had both alleles from the Gir breed (GG). In high-ΔRT animals, the average proportion of animals for HH and GG were 1.4 and 50.2%, respectively. This study allowed the identification of candidate genes for ΔRT in Gir × Holstein crossbred animals. According to the BOA approach, Holstein breed alleles could be associated with better response to heat stress effects, which could be explained by the fact that Holstein animals are more affected by heat stress than Gir animals and thus require a genetic architecture to defend the body from the deleterious effects of heat stress. Future studies can provide further knowledge to uncover the genetic architecture underlying heat stress in crossbred cattle.

Pest kill rate as aggregate evaluation criterion to rank biological control agents: A case study with Neotropical predators of Tuta absoluta on tomato
Lenteren, J.C. Van; Bueno, V.H.P. ; Burgio, G. ; Lanzoni, A. ; Montes, F.C. ; Silva, D.B. ; Jong, P.W. De; Hemerik, L. - \ 2019
Bulletin of Entomological Research (2019). - ISSN 0007-4853
biological control - Campyloneuropsis infumatus - Engytatus varians - Macrolophus basicornis - Miridae - natural enemy efficacy - natural enemy evaluation criteria - South American tomato moth

Tuta absoluta (Meyrick), a key pest of tomato, is quickly spreading over the world and biological control is considered as one of the control options. Worldwide more than 160 species of natural enemies are associated with this pest, and an important challenge is to quickly find an effective biocontrol agent from this pool of candidate species. Evaluation criteria for control agents are presented, with the advantages they offer for separating potentially useful natural enemies from less promising ones. Next, an aggregate parameter for ranking agents is proposed: the pest kill rate k m . We explain why the predator's intrinsic rate of increase cannot be used for comparing the control potential of predators or parasitoids, while k m can be used to compare both types of natural enemies. As an example, kill rates for males, females and both sexes combined of three Neotropical mirid species (Campyloneuropsis infumatus (Carvalho), Engytatus varians (Distant) and Macrolophus basicornis (Stål)) were determined, taking all life-history data (developmental times, survival rates, total nymphal and adult predation, sex ratios and adult lifespan) into account. Based on the value for the intrinsic rate of increase (r m ) for T. absoluta and for the kill rate k m of the predators, we predict that all three predators are potentially able to control the pest, because their k m values are all higher than the r m of the pest. Using only k m values, we conclude that E. varians is the best candidate for control of T. absoluta on tomato, with C. infumatus ranking second and M. basicornis last.

Recent insights on uncertainties present in integrated catchment water quality modelling
Tscheikner-Gratl, Franz ; Bellos, Vasilis ; Schellart, Alma ; Moreno-Rodenas, Antonio ; Muthusamy, Manoranjan ; Langeveld, Jeroen ; Clemens, Francois ; Benedetti, Lorenzo ; Rico-Ramirez, Miguel Angel ; Carvalho, Rita Fernandes de; Breuer, Lutz ; Shucksmith, James ; Heuvelink, Gerard B.M. ; Tait, Simon - \ 2019
Water Research 150 (2019). - ISSN 0043-1354 - p. 368 - 379.
Complexity management - Integrated catchment modelling - Sub-models of integrated modelling - Uncertainty - Water quality

This paper aims to stimulate discussion based on the experiences derived from the QUICS project (Quantifying Uncertainty in Integrated Catchment Studies). First it briefly discusses the current state of knowledge on uncertainties in sub-models of integrated catchment models and the existing frameworks for analysing uncertainty. Furthermore, it compares the relative approaches of both building and calibrating fully integrated models or linking separate sub-models. It also discusses the implications of model linkage on overall uncertainty and how to define an acceptable level of model complexity. This discussion includes, whether we should shift our attention from uncertainties due to linkage, when using linked models, to uncertainties in model structure by necessary simplification or by using more parameters. This discussion attempts to address the question as to whether there is an increase in uncertainty by linking these models or if a compensation effect could take place and that overall uncertainty in key water quality parameters actually decreases. Finally, challenges in the application of uncertainty analysis in integrated catchment water quality modelling, as encountered in this project, are discussed and recommendations for future research areas are highlighted.

Removal of soil biota alters soil feedback effects on plant growth and defense chemistry
Wang, Minggang ; Ruan, Weibin ; Kostenko, Olga ; Carvalho, Sabrina ; Hannula, S.E. ; Mulder, Patrick P.J. ; Bu, Fengjiao ; Putten, Wim H. van der; Bezemer, T.M. - \ 2019
New Phytologist 221 (2019)3. - ISSN 0028-646X - p. 1478 - 1491.
fractionation - Jacobaea vulgaris - plant–soil feedback (PSF) - pyrrolizidine alkaloids (PAs) - soil biota - spectral reflectance

We examined how the removal of soil biota affects plant–soil feedback (PSF) and defense chemistry of Jacobaea vulgaris, an outbreak plant species in Europe containing the defense compounds pyrrolizidine alkaloids (PAs). Macrofauna and mesofauna, as well as fungi and bacteria, were removed size selectively from unplanted soil or soil planted with J. vulgaris exposed or not to above- or belowground insect herbivores. Wet-sieved fractions, using 1000-, 20-, 5- and 0.2-μm mesh sizes, were added to sterilized soil and new plants were grown. Sieving treatments were verified by molecular analysis of the inocula. In the feedback phase, plant biomass was lowest in soils with 1000- and 20-μm inocula, and soils conditioned with plants gave more negative feedback than without plants. Remarkably, part of this negative PSF effect remained present in the 0.2-μm inoculum where no bacteria were present. PA concentration and composition of plants with 1000- or 20-μm inocula differed from those with 5- or 0.2-μm inocula, but only if soils had been conditioned by undamaged plants or plants damaged by aboveground herbivores. These effects correlated with leaf hyperspectral reflectance. We conclude that size-selective removal of soil biota altered PSFs, but that these PSFs were also influenced by herbivory during the conditioning phase.

Towards efficient workflows for soil data standardisation and model integration
Batjes, Niels ; Carvalho Ribeiro, Eloi ; Oostrum, Ad van; Kempen, Bas ; Bosch, Rik van den - \ 2018
Data from: Disturbance intensity is a stronger driver of biomass recovery than remaining tree-community attributes in a managed Amazonian forest
Avila, Angel L. de; Sande, M.T. van der; Dormann, C.F. ; Pena Claros, M. ; Poorter, L. ; Mazzei, Lucas ; Ruschel, Ademir Roberto ; Silva, José N.M. ; Carvalho, J.O.P. ; Bauhus, J. - \ 2018
University of Freiburg
biomass-ratio hypothesis - biomass recovery - disturbance intensity - niche-complementarity hypothesis - stand thinning (refinement) - selective logging
1.Forest recovery following management interventions is important to maintain ecosystem functioning and the provision of ecosystem services. It remains, however, largely unclear how aboveground biomass (AGB) recovery of species-rich tropical forests is affected by disturbance intensity and post-disturbance (remaining) tree-community attributes, following logging and thinning interventions. 2.We investigated whether annual AGB increment (∆AGB) decreases with management-related disturbance intensity (disturbance hypothesis), and increases with the diversity (niche-complementarity hypothesis) and the community-weighted mean (CWM) of acquisitive traits of dominant species (biomass-ratio hypothesis) in the remaining tree community. 3.We analysed data from a long-term forest-management experiment in the Brazilian Amazon over two recovery periods: post-logging (1983-1989) and post-thinning (1995-2012). We computed the ∆AGB of surviving trees, recruit trees and of the total tree community. Disturbance intensity was quantified as basal area reduction and basal area remaining. Remaining diversity (taxonomic, functional and structural) and CWM of five functional traits linked to biomass productivity (specific leaf area, leaf nitrogen and phosphorous concentration, leaf toughness and wood density) were calculated for the post-intervention inventories. Predictors were related to response variables using multiple linear regressions and structural equation modelling. 4.We found support for the disturbance hypothesis in both recovery periods. AGB increment of survivors and of the total tree community increased with basal area remaining, indicating the importance of remaining growing stock for biomass recovery. Conversely, AGB increment of recruit trees increased with basal area reduction because changes in forest structure increased resource availability for young trees. We did not find consistent support for the niche-complementarity and biomass-ratio hypotheses, possibly because of a high redundancy in these extremely species-rich forests. 5.Synthesis and applications. The intensity of disturbance through management, expressed as basal area reduction and basal area remaining, was consistently more important for explaining forest biomass recovery following harvesting and thinning than remaining diversity or trait composition. This points to the importance of controlling logging and thinning intensity in forests of the eastern Amazon. Low to moderate harvesting intensities permitted by the current legislation for the Brazilian Amazon (30 m³ ha−1) will likely not impair biomass recovery in these forests.
Adult lifetime predation of Tuta absoluta eggs by three Neotropical mirid predators on tomato
Lenteren, Joop C. van; Bueno, Vanda Helena Paes ; Montes, Flavio Cardoso ; Hemerik, Lia ; Jong, Peter W. de - \ 2018
Bulletin of Insectology 71 (2018)2. - ISSN 1721-8861 - p. 179 - 188.
Biological control - Engytatus varians - Infumatus - Macrolophus basicornis - Miridae - Tomato borer

Tuta absoluta (Meyrick), a key pest of tomato, is quickly spreading over the world. Here we report lifetime predation of T. absoluta eggs by adults of three Neotropical mirid species [Campyloneuropsis infumatus (Carvalho), Engytatus varians (Distant) and Macrolophus basicornis (Stal)]. Prey eggs were offered ad libitum on a tomato leaflet at 24 ± 1 °C, 70 ± 10% RH and 12-h photophase. Daily, the number of eggs consumed by adults was noted. Observations were terminated after all adults had died. Total adult lifetime predation of T. absoluta eggs was 337, 313 and 339 for males, and 845, 668 and 934 for females of C. infumatus, E. varians and M. basicornis, respectively. Mean adult lifespan was 27 days for males and 24 for females of C. infumatus, 17 days for males and 14 for females of E. varians, and 30 days for males and 26 days for females of M. basicornis. Total and daily predation was significantly higher for females than for males, though lifespan was significantly longer for males than for females. The daily predation rates of C. infumatus and M. basicornis were similar, but were significantly lower than that of E. varians. Predation rates tended to decrease significantly with adult age for both sexes of all three species, except for males of M. basicornis, although proportions of explained variance were low (r2 < 0.24). Adult survival and egg predation data will later be combined with data about egg development time and survival, and nymphal development time, survival and egg predation to determine the pest kill rate of the three mirid species. The pest kill rate will then be used to predict which of the mirids might be best for control of T. absoluta on tomato. Eventually, experiments at practical tomato production conditions will show whether our predictions are correct.

Eighty Years of Mycopathologia: A Retrospective Analysis of Progress Made in Understanding Human and Animal Fungal Pathogens
Chaturvedi, Vishnu ; Bouchara, Jean Philippe ; Hagen, Ferry ; Alastruey-Izquierdo, Ana ; Badali, Hamid ; Bocca, Anamelia Lorenzetti ; Cano-Lira, Jose F. ; Cao, Cunwei ; Chaturvedi, Sudha ; Chotirmall, Sanjay H. ; Diepeningen, Anne D. Van; Gangneux, Jean Pierre ; Guinea, Jesus ; Hoog, Sybren De; Ilkit, Macit ; Kano, Rui ; Liu, Weida ; Martinez-Rossi, Nilce M. ; Souza Carvalho Melhem, Marcia De; Ono, Mario Augusto ; Ran, Yuping ; Ranque, Stephane ; Almeida Soares, Celia Maria De; Sugita, Takashi ; Thomas, Philip A. ; Vecchiarelli, Anna ; Wengenack, Nancy L. ; Woo, Patrick C.Y. ; Xu, Jianping ; Zancope-Oliveira, Rosely M. - \ 2018
Mycopathologia 183 (2018)6. - ISSN 0301-486X - p. 859 - 877.
Mycopathologia was founded in 1938 to ‘diffuse the understanding of fungal diseases in man and animals among mycologists.’ This was an important mission considering that pathogenic fungi for humans and animals represent a tiny minority of the estimated 1.5–5 million fungal inhabitants on Earth. These pathogens have diverged from the usual saprotrophic lifestyles of most fungi to colonize and infect humans and animals. Medical and veterinary mycology is the subdiscipline of microbiology that dwells into the mysteries of parasitic, fungal lifestyles. Among the oldest continuing scientific publications on the subject, Mycopathologia had its share of ‘classic papers’ since the first issue was published in 1938. An analysis of the eight decades of notable contributions reveals many facets of host–pathogen interactions among 183 volumes comprising about 6885 articles. We have analyzed the impact and relevance of this body of work using a combination of citation tools (Google Scholar and Scopus) since no single citation metric gives an inclusive perspective. Among the highly cited Mycopathologia publications, those on experimental mycology accounted for the major part of the articles (36%), followed by diagnostic mycology (16%), ecology and epidemiology (15%), clinical mycology (14%), taxonomy and classification (10%), and veterinary mycology (9%). The first classic publication, collecting nearly 200 citations, appeared in 1957, while two articles published in 2010 received nearly 150 citations each, which is notable for a journal covering a highly specialized field of study. An empirical analysis of the publication trends suggests continuing interests in novel diagnostics, fungal pathogenesis, review of clinical diseases especially with relevance to the laboratory scientists, taxonomy and classification of fungal pathogens, fungal infections and carriage in pets and wildlife, and changing ecology and epidemiology of fungal diseases around the globe. We anticipate that emerging and re-emerging fungal pathogens will continue to cause significant health burden in the coming decades. It remains vital that scientists and physicians continue to collaborate by learning each other’s language for the study of fungal diseases, and Mycopathologia will strive to be their partner in this increasingly important endeavor to its 100th anniversary in 2038 and beyond.
Cadmium associates with oxalate in calcium oxalate crystals and competes with calcium for translocation to stems in the cadmium bioindicator Gomphrena claussenii
Pongrac, Paula ; Serra, Tânia S. ; Castillo-Michel, Hiram ; Vogel-Mikuš, Katarina ; Arčon, Iztok ; Kelemen, Mitja ; Jenčič, Boštjan ; Kavčič, Anja ; Villafort Carvalho, Mina T. ; Aarts, Mark G.M. - \ 2018
Metallomics 10 (2018)11. - ISSN 1756-5901 - p. 1576 - 1584.

Cadmium (Cd) was shown to co-localise with calcium (Ca) in oxalate crystals in the stems and leaves of Cd tolerant Gomphrena claussenii, but Cd binding remained unresolved. Using synchrotron radiation X-ray absorption near edge spectroscopy we demonstrate that in oxalate crystals of hydroponically grown G. claussenii the vast majority of Cd is bound to oxygen ligands in oxalate crystals (>88%; Cd-O-C coordination) and the remaining Cd is bound to sulphur ligands (Cd-S-C coordination). Cadmium binding to oxalate does not depend on the amount of Ca supplied or from which organs the crystals originate (stems and mature leaves). By contrast, roots contain no oxalate crystals and therein Cd is bound predominantly by S ligands. The potential to remove Cd by extraction of Cd-rich oxalate crystals from plant material should be tested in phytoextraction or phytomining strategies.

Environmental benefits of farm- and district-scale crop-livestock integration: a European perspective
Leterme, Philippe ; Nesme, Thomas ; Regan, John T. ; Korevaar, H. - \ 2018
In: Agroecosystem diversity / Lemaire, Gilles, César De Faccio Carvalho, Paulo, Kronberg, Scott, Recous, Sylvie, Academic Press - ISBN 9780128110508 - p. 335 - 349.
Specialized farms and districts generally perform poorly when assessed in terms of environmental impact or ecosystem services provision. Well-managed synergies between crop and livestock production occurring either at the farm scale or at the district scale have the potential to limit environmental problems via, for example, nutrient cycle closure and diversified crop rotations and land uses. However, there is a lack of research using empirical farm data to quantify the actual benefits or drawbacks of crop-livestock integration strategies. Therefore, a farming system approach was used in the “Crops and Animal Together” project (FP7 Project CANTOGETHER) to assess diverse strategies of crop-livestock integration at both farm (10 farms in FR, NL, IT, IE, UK) and district levels (5 districts in ES, IE, FR, NL, CH). The district-level strategies assessed were (1) local exchange of materials among farms (grain, slurry); (2) provision of high-quality forages (cooperative dehydration facility); (3) land exchange between dairy and arable farms; and (4) animal exchanges between lowland and highland regions (heifer rearing). A selection of noncooperating baseline farms (specialized and, where available, mixed) were compared with specialized cooperating farms in each district.

Results confirmed that it was the physical integration and complementarity between crops and animals (e.g., home-grown feed, recycling of wastes as fertilizers), not just their coexistence, that was decisive for achieving improved environmental performance at the farm level. Unfortunately, integration at the farm level had the drawbacks of increased workload and reduced productivity and economic performance. At the district level, organization between farms through strategies such as those assessed generally improved productivity and economic performances. However, the potential ecologic benefits of cooperation at district level are restricted by a rebound effect: farmers choosing to use the resources made available via cooperation to intensify their operations as opposed to diversifying them or reducing inputs.

In spite of this intensification, cooperation led to environmental benefits by increasing input use efficiency and reducing environmental impacts of farming when expressed per unit of agricultural product produced. An important finding was that territorial cooperation appeared as a key strategy to enable the farms that have implemented a high level of integration between crop and livestock to recover sufficient profitability.
Genome-wide association studies for tick resistance in Bos taurus × Bos indicus crossbred cattle : A deeper look into this intricate mechanism
Otto, Pamela I. ; Guimarães, Simone E.F. ; Verardo, Lucas L. ; Azevedo, Ana Luísa S. ; Vandenplas, Jeremie ; Soares, Aline C.C. ; Sevillano, Claudia A. ; Veroneze, Renata ; Fatima A. Pires, Maria de; Freitas, Célio de; Prata, Márcia Cristina A. ; Furlong, John ; Verneque, Rui S. ; Martins, Marta Fonseca ; Panetto, João Cláudio C. ; Carvalho, Wanessa A. ; Gobo, Diego O.R. ; Silva, Marcos Vinícius G.B. da; Machado, Marco A. - \ 2018
Journal of Dairy Science 101 (2018)12. - ISSN 0022-0302 - p. 11020 - 11032.
breed of origin - gene network - genetic variance - Gir × Holstein crossbred
Rhipicephalus (Boophilus) microplus is the main cattle ectoparasite in tropical areas. Gir × Holstein crossbred cows are well adapted to different production systems in Brazil. In this context, we performed genome-wide association study (GWAS) and post-GWAS analyses for R. microplus resistance in an experimental Gir × Holstein F2 population. Single nucleotide polymorphisms (SNP) identified in GWAS were used to build gene networks and to investigate the breed of origin for its alleles. Tick artificial infestations were performed during the dry and rainy seasons. Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA) and single-step BLUP procedure was used for GWAS. Post-GWAS analyses were performed by gene ontology terms enrichment and gene transcription factors networks, generated from enriched transcription factors, identified from the promoter sequences of selected gene sets. The genetic origin of marker alleles in the F2 population was assigned using the breed of origin of alleles approach. Heritability estimates for tick counts were 0.40 ± 0.11 in the rainy season and 0.54 ± 0.11 in dry season. The top ten 0.5-Mbp windows with the highest percentage of genetic variance explained by SNP markers were found in chromosomes 10 and 23 for both the dry and rainy seasons. Gene network analyses allowed the identification of genes involved with biological processes relevant to immune system functions (TREM1, TREM2, and CD83). Gene-transcription factors network allowed the identification of genes involved with immune functions (MYO5A, TREML1, and PRSS16). In resistant animals, the average proportion of animals showing significant SNPs with paternal and maternal alleles originated from Gir breed was 44.8% whereas the proportion of animals with both paternal and maternal alleles originated from Holstein breed was 11.3%. Susceptible animals showing both paternal and maternal alleles originated from Holstein breed represented 44.6% on average, whereas both paternal and maternal alleles originated from Gir breed animals represented 9.3%. This study allowed us to identify candidate genes for tick resistance in Gir × Holstein crossbreds in both rainy and dry seasons. According to the origin of alleles analysis, we found that most animals classified as resistant showed 2 alleles from Gir breed, while the susceptible ones showed alleles from Holstein. Based on these results, the identified genes may be thoroughly investigated in additional experiments aiming to validate their effects on tick resistance phenotype in cattle.
Comparative effectiveness and injury to tomato plants of three neotropical mirid predators of tuta absoluta (Lepidoptera : Gelechiidae)
Lenteren, Joop C. van; Bueno, V.H.P. ; Calvo, F.J. ; Calixto, Ana M. ; Montes, Flavio C. - \ 2018
Journal of Economic Entomology 111 (2018)3. - ISSN 0022-0493 - p. 1080 - 1086.
Biological control - Miridae - Tomato borer - Zoophytophagy

Tuta absoluta (Meyrick; Lepidoptera: Gelechiidae) is a key pest of tomato and is quickly spreading over the world. We conducted an experiment aimed at evaluating the control capacity and risk for plant damage of three Neotropical mirid species, Campyloneuropsis infumatus (Carvalho; Hemiptera: Miridae), Engytatus varians (Distant; Hemiptera: Miridae) and Macrolophus basicornis (Stal; Hemiptera: Miridae) on T. absoluta infested tomato plants in large cages in an experimental greenhouse. During three successive periods of 9 wk each, we followed population development of the three mirids when exposed to T. absoluta, and of T. absoluta alone in separate cages in the greenhouse. We determined weekly the numbers of T. absoluta eggs and larvae per leaf, the number of mirid predators per leaf, the percentage of damaged leaves and fruits by T. absoluta, and the weight of fruits. Two of the mirid predators, C. infumatus and M. basicornis, successfully established on T. absoluta infested tomato plants and significantly reduced T. absoluta numbers, which ultimately resulted in an increased yield. These two mirid species hardly injured tomato plants or fruits as a result of plant feeding. Surprisingly, the species E. varians, which showed high predation rates in laboratory experiments, did not establish and reduce pest populations in any of the tests.

Crop traits drive soil carbon sequestration under organic farming
García-Palacios, Pablo ; Gattinger, Andreas ; Bracht-Jørgensen, Helene ; Brussaard, Lijbert ; Carvalho, Filipe ; Castro, Helena ; Clément, Jean Christophe ; Deyn, Gerlinde De; Hertefeldt, Tina D'; Foulquier, Arnaud ; Hedlund, Katarina ; Lavorel, Sandra ; Legay, Nicolas ; Lori, Martina ; Mäder, Paul ; Martínez-García, Laura B. ; Martins da Silva, Pedro ; Muller, Adrian ; Nascimento, Eduardo ; Reis, Filipa ; Symanczik, Sarah ; Paulo Sousa, José ; Milla, Rubén - \ 2018
Journal of Applied Ecology 55 (2018)5. - ISSN 0021-8901 - p. 2496 - 2505.
climate change mitigation - crop residue - ecological intensification - leaf nitrogen - meta-analysis - organic farming - resource economics traits - soil carbon stocks

Organic farming (OF) enhances top soil organic carbon (SOC) stocks in croplands compared with conventional farming (CF), which can contribute to sequester C. As farming system differences in the amount of C inputs to soil (e.g. fertilization and crop residues) are not enough to explain such increase, shifts in crop residue traits important for soil C losses such as litter decomposition may also play a role. To assess whether crop residue (leaf and root) traits determined SOC sequestration responses to OF, we coupled a global meta-analysis with field measurements across a European-wide network of sites. In the meta-analysis, we related crop species averages of leaf N, leaf-dry matter content, fine-root C and N, with SOC stocks and sequestration responses in OF vs. CF. Across six European sites, we measured the management-induced changes in SOC stocks and leaf litter traits after long-term ecological intensive (e.g. OF) vs. CF comparisons. Our global meta-analysis showed that the positive OF-effects on soil respiration, SOC stocks, and SOC sequestration rates were significant even in organic farms with low manure application rates. Although fertilization intensity was the main driver of OF-effects on SOC, leaf and root N concentrations also played a significant role. Across the six European sites, changes towards higher leaf litter N in CF also promoted lower SOC stocks. Our results highlight that crop species displaying traits indicative of resource-acquisitive strategies (e.g. high leaf and root N) increase the difference in SOC between OF and CF. Indeed, changes towards higher crop residue decomposability was related with decreased SOC stocks under CF across European sites. Synthesis and applications. Our study emphasizes that, with management, changes in crop residue traits contribute to the positive effects of organic farming (OF) on soil carbon sequestration. These results provide a clear message to land managers: the choice of crop species, and more importantly their functional traits (e.g. leave and root nitrogen), should be considered in addition to management practices and climate, when evaluating the potential of OF for climate change mitigation.

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