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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    Water use in greenhouse horticulture: efficiency and circularity
    Costa, Joaquim Miguel ; Berckmoes, Els ; Beerling, E.A.M. ; Nicol, Silvana ; Jose, Juan ; Garcia, Javier ; Cáceres, Rafaela - \ 2019
    EIP-AGRI (EIP-AGRI Focus Group – Circular horticulture Mini-paper ) - 19 p.
    J oaquim Miguel Costa , Els Berkmoes , E ll e n B e e rling, Silvana Nicol , Juan Jose, Javier Gar c ia , Rafaela C á ceres
    Circularity and/or Valorisation of Biomass: Crop Residues, By - products and Extraction of Molecules
    Grade, Stefanie ; Beerling, E.A.M. ; Blanco, Belen ; Cáceres, Rafaela ; Checa, Javier Garcia ; Lonardo, Sara Di; Lemmens, Patrick ; Magán, Juan José ; Vandecasteele, Bart ; Veberic, Robert - \ 2019
    EIP-AGRI (EIP-AGRI Focus Group – Circular horticulture Mini-paper ) - 14 p.
    Awareness raising and transfer of knowledge and technology in circular horticulture
    Beerling, E.A.M. ; Berckmoes, Els ; Cáceres, Rafaela ; Väninnen, Irene ; Garcia, Javier ; Gonzalez, Fransisco Egea - \ 2019
    EIP-AGRI (EIP-AGRI Focus Group – Circular horticulture Mini-paper ) - 14 p.
    E ll e n B e e r li n g , E l s B e r c k m o e s , R a f a e l a C á c e r e s , I r e n e V ä n i n n e n , J a v i e r Garcia, Fransisco Egea Gonzalez
    Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism
    Spang, Anja ; Stairs, Courtney W. ; Dombrowski, Nina ; Eme, Laura ; Lombard, Jonathan ; Caceres, Eva F. ; Greening, Chris ; Baker, Brett J. ; Ettema, Thijs J.G. - \ 2019
    Nature Microbiology 4 (2019). - ISSN 2058-5276 - p. 1138 - 1148.

    The origin of eukaryotes represents an unresolved puzzle in evolutionary biology. Current research suggests that eukaryotes evolved from a merger between a host of archaeal descent and an alphaproteobacterial endosymbiont. The discovery of the Asgard archaea, a proposed archaeal superphylum that includes Lokiarchaeota, Thorarchaeota, Odinarchaeota and Heimdallarchaeota suggested to comprise the closest archaeal relatives of eukaryotes, has helped to elucidate the identity of the putative archaeal host. Whereas Lokiarchaeota are assumed to employ a hydrogen-dependent metabolism, little is known about the metabolic potential of other members of the Asgard superphylum. We infer the central metabolic pathways of Asgard archaea using comparative genomics and phylogenetics to be able to refine current models for the origin of eukaryotes. Our analyses indicate that Thorarchaeota and Lokiarchaeota encode proteins necessary for carbon fixation via the Wood–Ljungdahl pathway and for obtaining reducing equivalents from organic substrates. By contrast, Heimdallarchaeum LC2 and LC3 genomes encode enzymes potentially enabling the oxidation of organic substrates using nitrate or oxygen as electron acceptors. The gene repertoire of Heimdallarchaeum AB125 and Odinarchaeum indicates that these organisms can ferment organic substrates and conserve energy by coupling ferredoxin reoxidation to respiratory proton reduction. Altogether, our genome analyses suggest that Asgard representatives are primarily organoheterotrophs with variable capacity for hydrogen consumption and production. On this basis, we propose the ‘reverse flow model’, an updated symbiogenetic model for the origin of eukaryotes that involves electron or hydrogen flow from an organoheterotrophic archaeal host to a bacterial symbiont.

    Considering the farm workforce as part of farmers' innovative behaviour: A key factor in inclusive on-farm processes of technology and practice adoption
    Cofre-Bravo, Gabriela ; Engler, Alejandra ; Klerkx, Laurens ; Leiva-Bianchi, Marcelo ; Adasme-Berrios, Cristian ; Caceres, Cristian - \ 2019
    Experimental Agriculture 55 (2019)5. - ISSN 0014-4797 - p. 723 - 737.
    The literature identifies multiple factors that can affect the adoption of new technologies and practices in agriculture to support farm innovation, such as farmers' socio-economic characteristics and the characteristics of the promoted technology, among others. It has, however, scarcely contemplated the role of the farm workforce in technology and practice adoption. The objective of this study is (i) to describe innovative behaviour and its relation with farmers' ability to collaborate with the workforce in the adoption process; and (ii) to associate this description with the level of adoption of certain technologies and practices. Structural equation modelling (bifactor model) was used to identify the components of innovative behaviour, and correlation analysis was used to determine the relationship between these components and adoption level. The results show that relevant components of innovative behaviour are farmers' ability to generate and implement new ideas, to extend their networks and to involve the workforce in the adoption process. Worker involvement proved to be a key factor within the definition of farmers' innovative behaviour, which additionally shows a positive and significant correlation with the level of adoption of technologies and practices. A main theoretical implication is that research on technology and practice adoption needs to move beyond looking at single owner-managers of (family) farms and incorporate workers into the unit of analysis. The practical and policy implications are that innovation support programmes should give more attention to workforce management, training and skills of owner-managers as transformative and inclusive leaders, as these are essential for technology and practice adoption, and more broadly for innovation capacity.
    Asgard archaea are the closest prokaryotic relatives of eukaryotes
    Spang, Anja ; Eme, Laura ; Saw, Jimmy H. ; Caceres, Eva F. ; Zaremba-Niedzwiedzka, Katarzyna ; Lombard, Jonathan ; Guy, Lionel ; Ettema, Thijs J.G. - \ 2018
    Plos Genetics 14 (2018)3. - ISSN 1553-7390
    Complex evolutionary history of translation elongation factor 2 and diphthamide biosynthesis in archaea and parabasalids
    Narrowe, Adrienne B. ; Spang, Anja ; Stairs, Courtney W. ; Caceres, Eva F. ; Baker, Brett J. ; Miller, Christopher S. ; Ettema, Thijs J.G. - \ 2018
    Genome Biology and Evolution 10 (2018)9. - ISSN 1759-6653 - p. 2380 - 2393.
    Asgard - Diphthamide - EF-2 - Korarchaeota - Metagenomics - Trichomonas

    Diphthamide is a modified histidine residue which is uniquely present in archaeal and eukaryotic elongation factor 2 (EF-2), an essential GTPase responsible for catalyzing the coordinated translocation of tRNA andmRNA through the ribosome. In part due to the roleofdiphthamide inmaintaining translational fidelity, itwas previously assumed that diphthamide biosynthesis genes (dph) are conserved across all eukaryotes and archaea. Here, comparative analysis of new and existing genomes reveals that some archaea (i.e., members of the Asgard superphylum,Geoarchaea, andKorarchaeota) and eukaryotes (i.e., parabasalids) lack dph. In addition, while EF-2 was thought to exist as a single copy in archaea, many of these dph-lacking archaeal genomes encode a second EF-2 paralog missing key residues required for diphthamide modification and for normal translocase function, perhaps suggesting functional divergence linked to loss of diphthamide biosynthesis. Interestingly, some Heimdallarchaeota previously suggested to be most closely related to the eukaryotic ancestormaintain dph genes and a single gene encoding canonical EF-2.Our findings reveal that the ability to produce diphthamide, once thought to be a universal feature in archaea and eukaryotes, has been lost multiple times during evolution, and suggest that anticipated compensatory mechanisms evolved independently.

    Pharmaceuticals and endocrine disruptors in raw and cooked seafood from European market : Concentrations and human exposure levels
    Álvarez-Muñoz, Diana ; Rodríguez-Mozaz, Sara ; Jacobs, Silke ; Serra-Compte, Albert ; Cáceres, Nuria ; Sioen, Isabelle ; Verbeke, Wim ; Barbosa, Vera ; Ferrari, Federico ; Fernández-Tejedor, Margarita ; Cunha, Sara ; Granby, Kit ; Robbens, Johan ; Kotterman, Michiel ; Marques, Antonio ; Barceló, Damià - \ 2018
    Environment International 119 (2018). - ISSN 0160-4120 - p. 570 - 581.
    Cooking - Dietary exposure - Endocrine disruptors - Pharmaceuticals - Risk - Seafood

    Pharmaceuticals (PhACs) and endocrine disrupting compounds (EDCs) are chemicals of emerging concern that can accumulate in seafood sold in markets. These compounds may represent a risk to consumers through effects on the human reproductive system, metabolic disorders, pathogenesis of breast cancer or development of microbial resistance. Measuring their levels in highly consumed seafood is important to assess the potential risks to human health. Besides, the effect of cooking on contaminant levels is relevant to investigate. Therefore, the objectives of this research were to study the presence and levels of PhACs and EDCs in commercially available seafood in the European Union market, to investigate the effect of cooking on contaminant levels, and to evaluate the dietary exposure of humans to these compounds through seafood consumption. A sampling survey of seafood from 11 European countries was undertaken. Twelve highly consumed seafood types were analysed raw and cooked with 3 analytical methods (65 samples, 195 analysis). PhACs were mostly not detectable or below quantification limits in seafood whereas EDCs were a recurrent group of contaminants quantified in the majority of the samples. Besides, cooking by steaming significantly increased their levels in seafood from 2 to 46-fold increase. Based on occurrence and levels, bisphenol A, methylparaben and triclosan were selected for performing a human exposure assessment and health risk characterisation through seafood consumption. The results indicate that the Spanish population has the highest exposure to the selected EDCs through seafood consumption, although the exposure via seafood remained below the current toxicological reference values.

    Tulipa gesneriana and Lilium longiflorum PEBP Genes and Their Putative Roles in Flowering Time Control
    Leeggangers, H.A.C.F. ; Rosilio-Brami, T. ; Nadal Bigas, Judit ; Rubin, N. ; Dijk, A.D.J. van; Nunez de Caceres Gonzalez, F.F. ; Saadon-Shitrit, S. ; Nijveen, H. ; Hilhorst, H.W.M. ; Immink, G.H. ; Zaccai, M. - \ 2018
    Plant and Cell Physiology 59 (2018)1. - ISSN 0032-0781 - p. 90 - 106.
    Floral induction in Tulipa gesneriana and Lilium longiflorum is triggered by contrasting temperature conditions, high and low temperature, respectively. In Arabidopsis, the floral integrator FLOWERING LOCUS T (FT), a member of the PEBP (phosphatidyl ethanolamine-binding protein) gene family, is a key player in flowering time control. In this study, one PEBP gene was identified and characterized in lily (LlFT) and three PEBP genes were isolated from tulip (TgFT1, TgFT2 and TgFT3). Overexpression of these genes in Arabidopsis thaliana resulted in an early flowering phenotype for LlFT and TgFT2, but a late flowering phenotype for TgFT1 and TgFT3. Overexpression of LlFT in L. longiflorum also resulted in an early flowering phenotype, confirming its proposed role as a flowering time-controlling gene. The tulip PEBP genes TgFT2 and TgFT3 have a similar expression pattern in tulip, but show opposite effects on the timing of flowering in Arabidopsis. Therefore, the difference between these two proteins was further investigated by interchanging amino acids thought to be important for the FT function. This resulted in the conversion of phenotypes in Arabidopsis upon overexpressing the substituted TgFT2 and TgFT3 genes, revealing the importance of these interchanged amino acid residues. Based on all obtained results, we hypothesize that LlFT is involved in creating meristem competence to flowering-related cues in lily, and TgFT2 is considered to act as a florigen involved in the floral induction in tulip. The function of TgFT3 remains unclear, but, based on our observations and phylogenetic analysis, we propose a bulb-specific function for this gene.
    Soil fertility and species traits, but not diversity, drive productivity and biomass stocks in a Guyanese tropical rainforest
    Sande, M.T. van der; Arets, E.J.M.M. ; Pena Claros, M. ; Hoosbeek, M.R. ; Caceres-Siani, Yasmani ; Hout, P. van de; Poorter, L. - \ 2018
    Functional Ecology 32 (2018)2. - ISSN 0269-8463 - p. 461 - 474.
    1.Tropical forests store and sequester large amounts of carbon in above- and below-ground plant biomass and soil organic matter (SOM), but how these are driven by abiotic and biotic factors remains poorly understood.
    2.Here, we test the effects of abiotic factors (light variation, caused by logging disturbance, and soil fertility) and biotic factors (species richness and functional trait composition) on biomass stocks (above-ground biomass, fine root biomass), SOM and productivity in a relatively monodominant Guyanese tropical rainforest. This forest grows on nutrient-poor soils and has few species that contribute most to total abundance. We, therefore, expected strong effects of soil fertility and species’ traits that determine resource acquisition and conservation, but not of diversity. We evaluated 6 years of data for 30 0.4-ha plots and tested hypotheses using structural equation models.
    3.Disturbance increased productivity but decreased above-ground biomass stocks. Soil phosphorus (P) enhanced above-ground biomass and productivity, whereas soil nitrogen reduced fine root biomass. In contrast to expectations, trait values representing acquisitive strategies (e.g. high leaf nutrient concentration) increased biomass stocks, possibly because they indicate higher nutrient absorption and thus higher biomass build-up. However, under harsh conditions where biomass increase is slow, acquisitive trait values may increase respiration and vulnerability to hazards and therefore increase biomass loss. As expected, species richness did not affect productivity.
    4.We conclude that light availability (through disturbance) and soil fertility—especially P—strongly limit forest biomass productivity and stocks in this Guyanese forest. Low P availability may cause strong environmental filtering, which in turn results in a small set of dominant species. As a result, community trait composition but not species richness determines productivity and stocks of biomass and SOM in tropical forest on poor soils.

    Asgard archaea illuminate the origin of eukaryotic cellular complexity
    Zaremba-Niedzwiedzka, Katarzyna ; Caceres, Eva F. ; Saw, Jimmy H. ; Bäckström, Disa ; Juzokaite, Lina ; Vancaester, Emmelien ; Seitz, Kiley W. ; Anantharaman, Karthik ; Starnawski, Piotr ; Kjeldsen, Kasper U. ; Stott, Matthew B. ; Nunoura, Takuro ; Banfield, Jillian F. ; Schramm, Andreas ; Baker, Brett J. ; Spang, Anja ; Ettema, Thijs J.G. - \ 2017
    Nature 541 (2017)7637. - ISSN 0028-0836 - p. 353 - 358.

    The origin and cellular complexity of eukaryotes represent a major enigma in biology. Current data support scenarios in which an archaeal host cell and an alphaproteobacterial (mitochondrial) endosymbiont merged together, resulting in the first eukaryotic cell. The host cell is related to Lokiarchaeota, an archaeal phylum with many eukaryotic features. The emergence of the structural complexity that characterizes eukaryotic cells remains unclear. Here we describe the Asgard superphylum, a group of uncultivated archaea that, as well as Lokiarchaeota, includes Thor-, Odin- A nd Heimdallarchaeota. Asgard archaea affiliate with eukaryotes in phylogenomic analyses, and their genomes are enriched for proteins formerly considered specific to eukaryotes. Notably, thorarchaeal genomes encode several homologues of eukaryotic membrane-trafficking machinery components, including Sec23/24 and TRAPP domains. Furthermore, we identify thorarchaeal proteins with similar features to eukaryotic coat proteins involved in vesicle biogenesis. Our results expand the known repertoire of eukaryote-specific proteins in Archaea, indicating that the archaeal host cell already contained many key components that govern eukaryotic cellular complexity.

    The novel bacterial phylum Calditrichaeota is diverse, widespread and abundant in marine sediments and has the capacity to degrade detrital proteins
    Marshall, Ian P.G. ; Starnawski, Piotr ; Cupit, Carina ; Fernández Cáceres, Eva ; Ettema, Thijs J.G. ; Schramm, Andreas ; Kjeldsen, Kasper U. - \ 2017
    Environmental Microbiology Reports 9 (2017)4. - ISSN 1758-2229 - p. 397 - 403.

    Calditrichaeota is a recently recognized bacterial phylum with three cultured representatives, isolated from hydrothermal vents. Here we expand the phylogeny and ecology of this novel phylum with metagenome-derived and single-cell genomes from six uncultivated bacteria previously not recognized as members of Calditrichaeota. Using 16S rRNA gene sequences from these genomes, we then identified 322 16S rRNA gene sequences from cultivation-independent studies that can now be classified as Calditrichaeota for the first time. This dataset was used to re-analyse a collection of 16S rRNA gene amplicon datasets from marine sediments showing that the Calditrichaeota are globally distributed in the seabed at high abundance, making up to 6.7% of the total bacterial community. This wide distribution and high abundance of Calditrichaeota in cold marine sediment has gone unrecognized until now. All Calditrichaeota genomes show indications of a chemoorganoheterotrophic metabolism with the potential to degrade detrital proteins through the use of extracellular peptidases. Most of the genomes contain genes encoding proteins that confer O2 tolerance, consistent with the relatively high abundance of Calditrichaeota in surficial bioturbated part of the seabed and, together with the genes encoding extracellular peptidases, suggestive of a general ecophysiological niche for this newly recognized phylum in marine sediment.

    Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life
    Spang, Anja ; Caceres, Eva F. ; Ettema, Thijs J.G. - \ 2017
    Science 357 (2017)6351. - ISSN 0036-8075

    About 40 years ago, Archaea were recognized as a major prokaryotic domain of life besides Bacteria. Recently, cultivation-independent sequencing methods have produced a wealth of genomic data for previously unidentified archaeal lineages, several of which appear to represent newly revealed branches in the tree of life. Analyses of some recently obtained genomes have uncovered previously unknown metabolic traits and provided insights into the evolution of archaea and their relationship to eukaryotes. On the basis of our current understanding, much archaeal diversity still defies genomic exploration. Efforts to obtain and study genomes and enrichment cultures of uncultivated microbial lineages will likely further expand our knowledge about archaeal phylogenetic and metabolic diversity and their cell biology and ecological function.

    Functional reconstruction of a eukaryotic-like E1/E2/(RING) E3 ubiquitylation cascade from an uncultured archaeon
    Hennell James, Rory ; Caceres, Eva F. ; Escasinas, Alex ; Alhasan, Haya ; Howard, Julie A. ; Deery, Michael J. ; Ettema, Thijs J.G. ; Robinson, Nicholas P. - \ 2017
    Nature Communications 8 (2017)1. - ISSN 2041-1723

    The covalent modification of protein substrates by ubiquitin regulates a diverse range of critical biological functions. Although it has been established that ubiquitin-like modifiers evolved from prokaryotic sulphur transfer proteins it is less clear how complex eukaryotic ubiquitylation system arose and diversified from these prokaryotic antecedents. The discovery of ubiquitin, E1-like, E2-like and small-RING finger (srfp) protein components in the Aigarchaeota and the Asgard archaea superphyla has provided a substantive step toward addressing this evolutionary question. Encoded in operons, these components are likely representative of the progenitor apparatus that founded the modern eukaryotic ubiquitin modification systems. Here we report that these proteins from the archaeon Candidatus 'Caldiarchaeum subterraneum' operate together as a bona fide ubiquitin modification system, mediating a sequential ubiquitylation cascade reminiscent of the eukaryotic process. Our observations support the hypothesis that complex eukaryotic ubiquitylation signalling pathways have developed from compact systems originally inherited from an archaeal ancestor.

    Soil fertility and species traits, but not diversity, drive productivity and biomass stocks in a Guyanese tropical rainforest
    Sande, M.T. van der; Arets, E.J.M.M. ; Pena Claros, M. ; Hoosbeek, M.R. ; Caceres-Siani, Yasmani ; Hout, P. van der; Poorter, L. - \ 2017
    biomass - soil fertility
    In this study, we test the effects of abiotic factors (light variation, caused by logging disturbance, and soil fertility) and biotic factors (species richness and functional trait composition) on biomass stocks (aboveground biomass, fine root biomass), SOM and productivity in a relatively monodominant Guyanese tropical rainforest. This forest grows on nutrient-poor soils and has few species that contribute most to total abundance. We therefore expected strong effects of soil fertility and species’ traits that determine resource acquisition and conservation, but not of diversity. We evaluated 6 years of data for 30 0.4-ha plots and tested hypotheses using structural equation models. Our results indicate that light availability (through disturbance) and soil fertility – especially P – strongly limit forest biomass productivity and stocks in this Guyanese forest. Low P availability may cause strong environmental filtering, which in turn results in a small set of dominant species. As a result, community trait composition but not species richness determines productivity and stocks of biomass and SOM in tropical forest on poor soils.
    Examining variation in the leaf mass per area of dominant species across two contrasting tropical gradients in light of community assembly
    Neyret, Margot ; Bentley, Lisa Patrick ; Oliveras Menor, Imma ; Marimon, Beatriz S. ; Marimon-Junior, Ben Hur ; Almeida de Oliveira, Edmar ; Barbosa Passos, Fábio ; Castro Ccoscco, Rosa ; Santos, Josias dos; Matias Reis, Simone ; Morandi, Paulo S. ; Rayme Paucar, Gloria ; Robles Cáceres, Arturo ; Valdez Tejeira, Yolvi ; Yllanes Choque, Yovana ; Salinas, Norma ; Shenkin, Alexander ; Asner, Gregory P. ; Díaz, Sandra ; Enquist, Brian J. ; Malhi, Yadvinder - \ 2016
    Ecology and Evolution 6 (2016)16. - ISSN 2045-7758 - p. 5674 - 5689.
    Community assembly - environmental filtering - interspecific variation - intraspecific variation - leaf mass per area - limiting similarity - T-statistics - tropical forests

    Understanding variation in key functional traits across gradients in high diversity systems and the ecology of community changes along gradients in these systems is crucial in light of conservation and climate change. We examined inter- and intraspecific variation in leaf mass per area (LMA) of sun and shade leaves along a 3330-m elevation gradient in Peru, and in sun leaves across a forest–savanna vegetation gradient in Brazil. We also compared LMA variance ratios (T-statistics metrics) to null models to explore internal (i.e., abiotic) and environmental filtering on community structure along the gradients. Community-weighted LMA increased with decreasing forest cover in Brazil, likely due to increased light availability and water stress, and increased with elevation in Peru, consistent with the leaf economic spectrum strategy expected in colder, less productive environments. A very high species turnover was observed along both environmental gradients, and consequently, the first source of variation in LMA was species turnover. Variation in LMA at the genus or family levels was greater in Peru than in Brazil. Using dominant trees to examine possible filters on community assembly, we found that in Brazil, internal filtering was strongest in the forest, while environmental filtering was observed in the dry savanna. In Peru, internal filtering was observed along 80% of the gradient, perhaps due to variation in taxa or interspecific competition. Environmental filtering was observed at cloud zone edges and in lowlands, possibly due to water and nutrient availability, respectively. These results related to variation in LMA indicate that biodiversity in species rich tropical assemblages may be structured by differential niche-based processes. In the future, specific mechanisms generating these patterns of variation in leaf functional traits across tropical environmental gradients should be explored.

    Old-growth Neotropical forests are shifting in species and trait composition
    Sande, M.T. van der; Arets, E.J.M.M. ; Pena Claros, M. ; Avila, L.A. ; Roopsind, A. ; Mazzei, L. ; Ascarrunz, N. ; Finegan, B. ; Alarcón, A. ; Caceres-Siani, Yasmani ; Licona, J.C. ; Ruschel, A.R. ; Toledo, M. ; Poorter, L. - \ 2016
    disturbance - drought - environmental gradients - forest dynamicsfunctional traits - global change - rainfall - resource availability - soil fertility
    This dataset contains the underlaying data for the study: Tropical forests have long been thought to be in stable state, but recent insights indicate that global change is leading to shifts in forest dynamics and species composition. These shifts may be driven by environmental changes such as increased resource availability, increased drought stress, and/or recovery from past disturbances. The relative importance of these drivers can be inferred from analysing changes in trait values of tree communities. Here, we evaluate a decade of change in species and trait composition across five old-growth Neotropical forests in Bolivia, Brazil, Guyana and Costa Rica that cover large gradients in rainfall and soil fertility. To identify the drivers of compositional change, we used data from 29 permanent sample plots and measurements of 15 leaf, stem and whole-plant traits that are important for plant performance and should respond to global change drivers. We found that forests differ strongly in their community-mean trait values, resulting from differences in soil fertility and annual rainfall seasonality. The abundance of deciduous species with high specific leaf area increases from wet to dry forests. The community-mean wood density is high in the driest forests to protect xylem vessels against drought-cavitation, and is high in nutrient poor forests to increase wood longevity and enhance nutrient residence time in the plant. The species composition changed over time in three of the forests, and the community-mean wood density increased and the specific leaf area decreased in all forests, indicating that these forests are changing towards later successional stages dominated by slow-growing, shade-tolerant species. We did not see changes in other traits that could reflect responses to increased drought stress, such as increased drought-deciduousness or decreased maximum adult size, or that could reflect increased resource availability (CO2, rainfall or nitrogen). Changes in species and trait composition in these forests are, therefore, most likely caused by recovery from past disturbances. These compositional changes may also lead to shifts in ecosystem processes, such as a lower carbon sequestration and “slower” forest dynamics. For 29 permanent sample plots in two census years across five old-growth Neotropical forests in Bolivia, Brazil, Guyana and Costa Rica, the following data are available: values of 15 leaf, stem and whole-plant traits at the community-level, and the plot scores along two principal component axes that represent species composition.
    Old-growth Neotropical forests are shifting in species and trait composition
    Sande, M.T. van der; Arets, E.J.M.M. ; Pena Claros, M. ; Avila, L.A. ; Roopsind, A. ; Mazzei, L. ; Ascarrunz, N. ; Finegan, Bryan ; Alarcon, A. ; Caceres-Siani, Yasmani ; Licona, J.C. ; Ruschel, A.R. ; Toledo, Marisol ; Poorter, L. - \ 2016
    Ecological Monographs 86 (2016)2. - ISSN 0012-9615 - p. 228 - 243.
    disturbance; drought; environmental gradients; forest dynamics; functional traits; global change; rainfall; resource availability; soil fertility.
    Tropical forests have long been thought to be in stable state, but recent
    insights indicate that global change is leading to shifts in forest dynamics and species composition. These shifts may be driven by environmental changes such as increased resource availability, increased drought stress, and/or recovery from past disturbances.
    The relative importance of these drivers can be inferred from analyzing changes in trait values of tree communities. Here, we evaluate a decade of change in species and trait composition across five old-growth Neotropical forests in Bolivia, Brazil, Guyana, and Costa Rica that cover large gradients in rainfall and soil fertility. To identify the drivers of compositional change, we used data from 29 permanent sample plots and measurements of 15 leaf, stem, and whole-plant
    traits that are important for plant performance and should respond to global change drivers. We found that forests differ strongly in their community-mean
    trait values, resulting from differences in soil fertility and annual rainfall seasonality. The abundance of deciduous species with high specific leaf area
    increases from wet to dry forests. The community-mean wood density is high in the driest forests to protect xylem vessels against drought cavitation, and is high in nutrient-poor forests to increase wood longevity and enhance nutrient residence time in the plant. Interestingly, the species composition changed over time in three of the forests, and the community-mean wood density increased and the specific leaf area decreased in all forests, indicating that these forests are changing toward later successional stages dominated by slow-growing,
    shade-tolerant species. We did not see changes in other traits that could reflect responses to increased drought stress, such as increased drought deciduousness
    or decreased maximum adult size, or that could reflect increased resource availability (CO2, rainfall, or nitrogen). Changes in species and trait composition in these forests are therefore most likely caused by recovery from past disturbances. These compositional changes may also lead to shifts in ecosystem processes, such as a lower carbon sequestration and “slower” forest dynamics.
    A comperative framework for broad-scale plot-based vegetation classification : Book of abstracts. Poster
    Caceres, M. de; Chytry, M. ; Agrillo, E. ; Attore, F. ; Schaminee, J.H.J. - \ 2015
    In: Book of Abstracts. -
    A comparative framework for broad-scale plot-based vegetation classification
    Caceres, M. de; Chytry, M. ; Agrillo, E. ; Attore, F. ; Schaminee, J.H.J. - \ 2015
    Applied Vegetation Science 18 (2015)4. - ISSN 1402-2001 - p. 543 - 560.
    Aims:
    Classification of vegetation is an essential tool to describe, understand, predict and manage biodiversity. Given the multiplicity of approaches to classify vegetation, it is important to develop international consensus around a set of general guidelines and purpose-specific standard protocols. Before these goals can be achieved, however, it is necessary to identify and understand the different choices that are made during the process of classifying vegetation. This paper presents a framework to facilitate comparisons between broad-scale plot-based classification approaches.

    Results:
    Our framework is based on the distinction of four structural elements (plot record, vegetation type, consistent classification section and classification system) and two procedural elements (classification protocol and classification approach). For each element we describe essential properties that can be used for comparisons. We also review alternative choices regarding critical decisions of classification approaches; with a special focus on the procedures used to define vegetation types from plot records. We illustrate our comparative framework by applying it to different broad-scale classification approaches.

    Conclusions:
    Our framework will be useful for understanding and comparing plot-based vegetation classification approaches, as well as for integrating classification systems and their sections.
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