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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    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.

    “Nano” Regeneration: How Human Agency Intermediates Between Nature and Technology in Community-Based Energy
    Walther, Charlotte Marie ; Poldner, Kim ; Kopnina, Helen ; Dentoni, Domenico - \ 2020
    Organization & Environment (2020). - ISSN 1086-0266
    community-based energy - human agency - nano - nature - regeneration - technology

    This article provides a nano (hyperlocal) view of climate change mitigation by viewing regenerative organizing through the eyes (as well as bodies and senses, etc.) of the households engaged in community-based energy projects. By showing what humans make up for in the largely absent relationship between nature and technology in these projects, we envision an incremental extension of the literature on community-based energy. The radically different contribution we aim to make is a tripartite imbrication that brings in natural agency alongside the human and the technical but specifies precisely how nano (smaller than micro) embodied practices afford mis- and realignments.

    Plant functional trait response to environmental drivers across European temperate forest understorey communities
    Maes, S.L. ; Perring, M.P. ; Depauw, L. ; Bernhardt-Römermann, M. ; Blondeel, H. ; Brūmelis, G. ; Brunet, J. ; Decocq, G. ; Ouden, J. den; Govaert, S. ; Härdtle, W. ; Hédl, R. ; Heinken, T. ; Heinrichs, S. ; Hertzog, L. ; Jaroszewicz, B. ; Kirby, K. ; Kopecký, M. ; Landuyt, D. ; Máliš, F. ; Vanneste, T. ; Wulf, M. ; Verheyen, K. - \ 2020
    Plant Biology 22 (2020)3. - ISSN 1435-8603 - p. 410 - 424.
    Global environmental change - ground vegetation - herbaceous layer - plant–soil relations - regeneration - resource acquisition

    Functional traits respond to environmental drivers, hence evaluating trait-environment relationships across spatial environmental gradients can help to understand how multiple drivers influence plant communities. Global-change drivers such as changes in atmospheric nitrogen deposition occur worldwide, but affect community trait distributions at the local scale, where resources (e.g. light availability) and conditions (e.g. soil pH) also influence plant communities. We investigate how multiple environmental drivers affect community trait responses related to resource acquisition (plant height, specific leaf area (SLA), woodiness, and mycorrhizal status) and regeneration (seed mass, lateral spread) of European temperate deciduous forest understoreys. We sampled understorey communities and derived trait responses across spatial gradients of global-change drivers (temperature, precipitation, nitrogen deposition, and past land use), while integrating in-situ plot measurements on resources and conditions (soil type, Olsen phosphorus (P), Ellenberg soil moisture, light, litter mass, and litter quality). Among the global-change drivers, mean annual temperature strongly influenced traits related to resource acquisition. Higher temperatures were associated with taller understoreys producing leaves with lower SLA, and a higher proportional cover of woody and obligate mycorrhizal (OM) species. Communities in plots with higher Ellenberg soil moisture content had smaller seeds and lower proportional cover of woody and OM species. Finally, plots with thicker litter layers hosted taller understoreys with larger seeds and a higher proportional cover of OM species. Our findings suggest potential community shifts in temperate forest understoreys with global warming, and highlight the importance of local resources and conditions as well as global-change drivers for community trait variation.

    Fire effects and ecological recovery pathways of tropical montane cloud forests along a time chronosequence
    Oliveras, Imma ; Román-Cuesta, Rosa M. ; Urquiaga-Flores, Erickson ; Quintano Loayza, Jose A. ; Kala, Jose ; Huamán, Vicky ; Lizárraga, Nohemi ; Sans, Guissela ; Quispe, Katia ; Lopez, Efrain ; Lopez, David ; Cuba Torres, Israel ; Enquist, Brian J. ; Malhi, Yadvinder - \ 2018
    Global Change Biology 24 (2018)2. - ISSN 1354-1013 - p. 758 - 772.
    carbon allocation - forest structure - metabolic scaling theory - regeneration - species diversity
    Tropical montane cloud forests (TMCFs) harbour high levels of biodiversity and large carbon stocks. Their location at high elevations make them especially sensitive to climate change, because a warming climate is enhancing upslope species migration, but human disturbance (especially fire) may in many cases be pushing the treeline downslope. TMCFs are increasingly being affected by fire, and the long-term effects of fire are still unknown. Here, we present a 28-year chronosequence to assess the effects of fire and recovery pathways of burned TMCFs, with a detailed analysis of carbon stocks, forest structure and diversity. We assessed rates of change of carbon (C) stock pools, forest structure and tree-size distribution pathways and tested several hypotheses regarding metabolic scaling theory (MST), C recovery and biodiversity. We found four different C stock recovery pathways depending on the selected C pool and time since last fire, with a recovery of total C stocks but not of aboveground C stocks. In terms of forest structure, there was an increase in the number of small stems in the burned forests up to 5–9 years after fire because of regeneration patterns, but no differences on larger trees between burned and unburned plots in the long term. In support of MST, after fire, forest structure appears to approximate steady-state size distribution in less than 30 years. However, our results also provide new evidence that the species recovery of TMCF after fire is idiosyncratic and follows multiple pathways. While fire increased species richness, it also enhanced species dissimilarity with geographical distance. This is the first study to report a long-term chronosequence of recovery pathways to fire suggesting faster recovery rates than previously reported, but at the expense of biodiversity and aboveground C stocks.
    Mechanisms of vegetative propagation in bulbs : a molecular approach
    Moreno-Pachón, Natalia - \ 2017
    Wageningen University. Promotor(en): R.G.H. Immink, co-promotor(en): H.W.M. Hilhorst. - Wageningen : Wageningen University - ISBN 9789463437011 - 178
    ornamental bulbs - tulipa - lilium - vegetative propagation - flowering date - gene regulation - genes - transcriptomes - dna sequencing - regeneration - shoot apices - bloembollen - tulipa - lilium - vegetatieve vermeerdering - bloeidatum - genregulatie - genen - transcriptomen - dna-sequencing - verjonging - scheuttoppen

    Vegetative propagation is very important for the survival of species with long juvenile and adult vegetative phases, as it is the case for bulbous plants. Bulbous plants are ornamental geophytes with a bulb as an underground storage organ. Among flower bulbs, tulip and lily are the two commercially leading plants in The Netherlands. Tulip propagates vegetatively via axillary bud outgrowth, while lily propagates via adventitious bulblet formation. The vegetative propagation rate in tulip is very low due to the limited amount of axillary buds that will grow successfully. Moreover, tulip is very recalcitrant to in vitro regeneration. On the other hand, lily propagates efficiently via adventitious bulblet formation, either naturally from the underground portion of the stem of the apical bud, or artificially from detached bulb scales.

    This thesis study aimed to understand how axillary bud outgrowth is controlled in tulip bulbs and how regeneration capacity is established in lily bulb scales. As a first step towards these goals, the state of the art of the molecular control of sexual and vegetative reproduction was reviewed for model species. Moreover, two approaches, “bottom-up” and “top-down”, to transfer the knowledge from model to non-model species were described (Chapter 2). In short, the “bottom-up” approach usually goes from individual genes to systems, assuming conservation of molecular pathways and using sequence homology searches to identify candidate genes. ”Top-down” methodologies go from systems to genes, and are based on large scale transcriptome profiling via e.g. microarrays or RNA sequencing, followed by the identification of associations between phenotypes, genes, and gene expression patterns and levels.

    Next (Chapter 3), two sets of high quality transcriptomes, one for tulip and one for lily were generated from a collection of several tissues using the Illumina HiSeq 2000 platform. Several assembly filtering parameters were applied, to highlight the limitations of stringent but routinely used filtering in de novo transcriptome assembly. The final created transcriptomes were made publicly available via a user friendly Transcriptome browser ( and their usefulness was exemplified by a search for all potential transcription factors in lily and tulip, with special focus on the TCP transcription factor family.

    One TCP member was of special interest because it has proven to integrate several pathways that control axillary bud outgrowth in a wide range of species. It is called TEOSINTE BRANCHED 1 (TB1) in monocots and BRNACHED 1 (BRC1) in dicots. A Tulipa gesneriana TB1 transcript was identified from the generated transcriptome and subsequently, tulip axillary bud outgrowth was studied through a “bottom-up” approach (Chapter 4). The degree of axillary bud outgrowth in tulip determines the success of their vegetative propagation. However the number of axillary meristems in one bulb is low –six on average– and not all of them seem to have the same growth capacity. The combination of physiological and targeted molecular experiments indicated that the first two inner located buds do not seem to experience dormancy (assessed by weight increase and TgTB1expression) at any point of the growth cycle, while mid-located buds enter dormancy by the end of the growing season. Moreover it was shown that TgTB1 expression in tulip bulbs can be modulated by sucrose, cytokinin and strigolactone, just as it has been reported for other species. However, the limited growth of mid-located buds even when their TgTB1 expression was naturally or artificially downregulated, pointed at other factors, probably physical, inhibiting their growth.

    Next, the remarkable regeneration capacity of lily by initiating de novo shoot meristems from excised bulb scales without the addition of exogenous hormones or growth regulators was studied using a “top-down” approach (Chapter 5). An extensive and comprehensive transcriptome set was generated from lily bulb scales in a time-series using two cultivars and two explant types, all differing in regeneration capacity. This set up provided first insight in the key molecular process underlying pro-meristem induction and meristem initiation in lily. We found that wounding activates a very fast regeneration response, probably mediated by APETALA2/ETHYLENE RESPONSIVE FACTORS (AP2/ERF,) such as LoERF115 and WOUND INDUCED DEDIFFERENTIATION 2 (LoWIND2), which in turn might mediate polar auxin re-distribution, cell proliferation and de-differentiation. Moreover, the timing and level of induction of shoot meristem regulators, such as ENHANCER OF SHOOT REGENERATION 2 (LoESR2) and SHOOT MERISTEMLESS (LoSTM) correlated with the regeneration capacity of the scale.

    Regardless the regeneration capacity of the different explants e.g. cultivar or position within the scale, regeneration occurs at the proximal-adaxial side of the bulb scale, right on top of the excision line. Thus the possible cellular and physiological factors granting lily bulb scales their competence to regenerate was investigated (Chapter 6). We found that the adaxial parenchyma tissue seems to be more competent than the abaxial tissue, partially because of higher number of secondary veins and larger cell population than the abaxial parenchyma region. It was proposed that upon explant excision, the polar auxin transport is disrupted, creating an auxin maximum at the excision line, which might create a gradient of cell divisions favouring the adaxial parenchyma tissue. The direction of this cell division gradient proved to be negatively affected by the absence of the adaxial epidermis. Moreover, explants without epidermis reduced dramatically their regeneration capacity, and lost the typical proximal-adaxial orientation of regeneration. Thus, a better understanding of the composition and physiology of the epidermis in lily bulb scales is essential to identify the regeneration stimulating signals originating from this tissue layer in Lilium sp.

    Finally in Chapter 7, integration of all the results was done and I addressed how this may contributes to the fundamental and applied understanding of vegetative propagation in bulbous plants. Also, some challenges are discussed, for example, the complexity in the architecture of tulip bulbs and how this influences ways for improving its rate of axillary bud outgrowth. The challenge to prove the findings of this thesis through functional analysis is also discussed and the possibility of using transient virus-induced gene silencing is highlighted. Moreover, the potential of lily bulb scales as a model system to study some aspects of de novo regeneration, as well as to study the recalcitrance of in vitro propagation is highlighted, supporting the idea that more “omics” data and biotechnological tools for bulbous plant research are necessary.

    Applied and fundamental aspects of BABY BOOM-mediated regeneration
    Heidmann, I.A. - \ 2015
    Wageningen University. Promotor(en): Gerco Angenent, co-promotor(en): Kim Boutilier. - Wageningen : Wageningen University - ISBN 9789462574663 - 180
    nicotiana tabacum - capsicum annuum - verjonging - transcriptiefactoren - somatische embryogenese - auxinen - moleculaire biologie - nicotiana tabacum - capsicum annuum - regeneration - transcription factors - somatic embryogenesis - auxins - molecular biology

    Keywords: Somatic embryogenesis, Transcription factor, AINTEGUMENTA-LIKE, BABY BOOM, BBM, Sweet Pepper Transformation

    Title: Applied and Fundamental Aspects of BBM-mediated Regeneration

    Author: Iris Heidmann

    Catergories: Plant regeneration, Plant transformation, transcription factor, somatic embryogenesis

    Plant regeneration from tissues or single cells is essential for plant propagation. Efficient regeneration can be archieved through somatic embryogenesis using the plant growth regulator auxin or overexpression of specific transcription factors, but the underlying mechanisms are poorly understood. The potency of the BABY BOOM (BBM) AINTEGUMENTA-LIKE transcription factor to induce somatic embryogenesis in crop (sweet pepper) and model species (tobacco) was investigated. It was found that the introduction of BBM into sweet pepper, which is recalcitrant for transformation, enhanced the regeneration of transgenic plants. Exogenous cytokinin was necessary to induce somatic embryogenesis in both tobacco and sweet pepper. The mechanism underlying BBM-mediated somatic embryogenesis was studied in Arabidopsis by identifying BBM target genes (ChIPSeq). Genes controlling zygotic embryo identity and maturation (LAFL), as well as auxin biosynthesis (TAA1, YUCCA) and transport (PIN) are BBM targets. Mutant analysis and chemical inhibition studies showed that these genes play positive roles in BBM-induced somatic embryogenesis.

    p21 Ablation in Liver Enhances DNA Damage, Cholestasis, and Carcinogenesis
    Ehedego, H. ; Boekschoten, M.V. ; Hu, W. ; Doler, C. ; Haybaeck, J. ; Gassler, N. ; Muller, M.R. ; Liedtke, C. ; Trautwein, C. - \ 2015
    Cancer Research 75 (2015)6. - ISSN 0008-5472 - p. 1144 - 1155.
    kinase inhibitor p21 - human hepatocellular-carcinoma - cell-cycle progression - rad51 overexpression - expression - p21(waf1/cip1) - mice - inflammation - regeneration - repair
    Genetic mouse studies suggest that the NF-¿B pathway regulator NEMO (also known as IKK¿) controls chronic inflammation and carcinogenesis in the liver. However, the molecular mechanisms explaining the function of NEMO are not well defined. Here, we report that overexpression of the cell-cycle regulator p21 is a critical feature of liver inflammation and carcinogenesis caused by the loss of NEMO. NEMO¿hepa mice develop chronic hepatitis characterized by increased hepatocyte apoptosis and proliferation that causes the development of fibrosis and hepatocellular carcinoma (HCC), similar to the situation in human liver disease. Having identified p21 overexpression in this model, we evaluated its role in disease progression and LPS-mediated liver injury in double mutant NEMO¿hepa/p21-/- mice. Eight-week-old NEMO¿hepa/p21-/- animals displayed accelerated liver damage that was not associated with alterations in cell-cycle progression or the inflammatory response. However, livers from NEMO¿hepa/p21-/- mice displayed more severe DNA damage that was further characterized by LPS administration correlating with higher lethality of the animals. This phenotype was attenuated by genetic ablation of the TNF receptor TNF-R1 in NEMO¿hepa/p21-/- mice, demonstrating that DNA damage is induced via TNF. One-year-old NEMO¿hepa/p21-/- mice displayed greater numbers of HCC and severe cholestasis compared with NEMO¿hepa animals. Therefore, p21 overexpression in NEMO¿hepa animals protects against DNA damage, acceleration of hepatocarcinogenesis, and cholestasis. Taken together, our findings illustrate how loss of NEMO promotes chronic liver inflammation and carcinogenesis, and they identify a novel protective role for p21 against the generation of DNA damage.
    Mature osteoblasts dedifferentiate in response to traumatic bone injury in the zebrafish fin and skull
    Geurtzen, K. ; Knopf, F. ; Wehner, D. ; Huitema, L.F.A. ; Schulte-Merker, S. ; Weidinger, G. - \ 2014
    Development 141 (2014). - ISSN 0950-1991 - p. 2225 - 2234.
    fibroblast-growth-factor - fracture repair - adult zebrafish - lining cells - regeneration - expression - defects - fate - gene - rats
    Zebrafish have an unlimited capacity to regenerate bone after fin amputation. In this process, mature osteoblasts dedifferentiate to osteogenic precursor cells and thus represent an important source of newly forming bone. By contrast, differentiated osteoblasts do not appear to contribute to repair of bone injuries in mammals; rather, osteoblasts form anew from mesenchymal stem cells. This raises the question whether osteoblast dedifferentiation is specific to appendage regeneration, a special feature of the lepidotrichia bone of the fish fin, or a process found more generally in fish bone. Here, we show that dedifferentiation of mature osteoblasts is not restricted to fin regeneration after amputation, but also occurs during repair of zebrafish fin fractures and skull injuries. In both models, mature osteoblasts surrounding the injury downregulate the expression of differentiation markers, upregulate markers of the pre-osteoblast state and become proliferative. Making use of photoconvertible Kaede protein as well as Cre-driven genetic fate mapping, we show that osteoblasts migrate to the site of injury to replace damaged tissue. Our findings suggest a fundamental role for osteoblast dedifferentiation in reparative bone formation in fish and indicate that adult fish osteoblasts display elevated cellular plasticity compared with mammalian bone-forming cells.
    The impact of large herbivores on woodland–grassland dynamics in fragmented landscapes: The role of spatial configuration and disturbance
    Schippers, P. ; Teeffelen, A.J.A. van; Verboom-Vasiljev, J. ; Vos, C.C. ; Kramer, K. ; Wallis de Vries, M.F. - \ 2014
    Ecological Complexity 17 (2014). - ISSN 1476-945X - p. 20 - 31.
    north temperate forests - red deer - population-dynamics - metapopulation dynamics - habitat fragmentation - distribution patterns - grazing systems - management - regeneration - resilience
    The vegetation structure of natural ecosystems is usually considered independent of their size and their location in the landscape. In this study, we examine the effect of size, spatial configuration and disturbances on the dynamic interactions of large herbivores and vegetation in a patchy environment using a metapopulation model. Simulations indicate that small, isolated or unfenced patches have low herbivore numbers and high tree cover whereas large, well-connected or fenced patches support high herbivore densities and are covered by grassland. Recovery of both herbivore numbers and forest cover in response to disturbance is slow (>100 years). These long recovery times are partly attributable to negative feedbacks between herbivore numbers and tree cover. When the population of large herbivores is disturbed, forest is able to expand, subsequently inhibiting herbivore population recovery. Likewise, forest disturbance allows herbivore population expansion, which inhibits forest recovery. Additionally, infrequent and limited disturbances like hunting and forest removal also affect the vegetation cover in patches of nature. Thus, our work indicates that the location and size of patches, together with disturbances, largely determine the structure of the vegetation in fragmented landscapes
    Age and light effects on seedling growth in two alternative secondary successions in central Amazonia
    Jakovac, A.C. ; Bentos, T.V. ; Mesquita, R.C.G. ; Williamson, G.B. - \ 2014
    Plant Ecology & Diversity 7 (2014)1-2. - ISSN 1755-0874 - p. 349 - 358.
    mahogany swietenia-macrophylla - cacao theobroma-cacao - tropical rain-forest - abandoned pastures - brazilian amazon - costa-rica - regeneration - communities - responses - environments
    Background : In central Amazonia, previous low intensity land use engenders succession dominated by Cecropia spp. which proceeds at high rates; however, at higher intensity of use succession is arrested and dominated by Vismia spp. over the long-term. Factors driving these two successional pathways are unknown. Aims : We aimed to elucidate seedling growth under the two alternative successional pathways. Methods : We experimentally determined the effects of successional age and photosynthetically active radiation (PAR) on relative height growth (RHG) of nine species of shade-tolerant tree seedlings in secondary forests dominated by Cecropia and Vismia, varying in age from 1–20 years. Results : In Cecropia-dominated successions, seedling RHG decreased with increasing successional age and with associated decreasing PAR. In Vismia-dominated successions, RHG was independent of successional age and PAR, and PAR did not change with successional age, being always higher than in Cecropia stands. The RHG of seedlings was lower in Vismia- than in Cecropia-dominated stands for similar PAR levels. Conclusions : Successional age and light availability affect seedlings growth differently in the two successional pathways. Unlike in Cecropia-dominated successions, in Vismia-dominated secondary forests seedling growth is limited by factors other than light. In a scenario of increasing land use intensity, constraints to seedling development in secondary forests can reduce species diversity in human-altered landscapes
    Pathways for resilience in Mediterranean cork oak land use systems
    Acácio, V.C. ; Holmgren, M. - \ 2014
    Annals of Forest Science 71 (2014)1. - ISSN 1286-4560 - p. 5 - 13.
    stress-gradient hypothesis - eastern iberian peninsula - arid ecosystems - south-america - el-nino - regeneration - facilitation - restoration - persistence - landscapes
    Context Loss of woodlands and degradation of vegetation and soil have been described for all Mediterranean-type ecosystems worldwide. In the Western Iberian Peninsula, overexploitation of evergreen cork oak land use systems has led to soil erosion, failures in oak recruitment, and loss of forests. Degraded and dry sites are quickly colonised by pioneer heathland rockrose (Cistus spp.) shrubs forming highly persistent patches. Aims Although traditionally shrublands have been considered as a transient successional state, we present evidence that they can represent persistent alternative states to former cork oak forests. Review trends and conclusions We first describe how Mediterranean vegetation evolved in the Iberian Peninsula and the role of fire and long-term human management as main disturbances. We then discuss alternative pathways through state-and-transition models indicating the ecological and land use variables that halt cork oak regeneration and recruitment and drive vegetation transitions towards persistent shrublands. Unless concerted management actions and restoration programmes are undertaken, the cork oak land use systems will not be sustainable
    An Improved Agrobacterium tumefaciens Mediated Transformation of Artemisia annua L. by Using Stem Internodes as Explants
    Tian, N.A. ; Liu, S. ; Huang, J. ; Krol, A.R. van der; Bouwmeester, H.J. ; Liu, Z. - \ 2013
    Czech Journal of Genetics and Plant Breeding 49 (2013)3. - ISSN 1212-1975 - p. 123 - 129.
    regeneration - malaria - plants - combination - drug - dna
    Transformation of Artemisia annua, which produces the sesquiterpenoid endoperoxide artemisinin widely used for the treatment of malaria, has been hampered by the low efficiency of adventitious shoot and root formation on a selective medium containing additional compounds for Agrobacterium decontamination. Here we identified several factors which were all shown to be of importance for optimization of Artemisia annua transformation. Results indicated that stem internodes showed better resistance capacity to Agrobacterium decontaminator than leaves did. Agrobacterium tumefaciens with an optical density (OD) value of 0.2–0.5 plus 100 µmol of acetosyringone per litre of solution gave the best transformation efficiency. Moreover, kanamycin at 30 mg/l in the culture medium was effective in suppressing the growth of non-transformed tissue. Furthermore, transgenic shoots required an early induction of rooting. In addition, dimethyl sulphoxide considerably improved the rooting of shoots. The present work provides rapid and reproducible transformation and regeneration of A. annua
    Can a fast­growing early­successional tree (Ochroma pyramidale, Malvaceae) accelerate forest succession?
    Vleut, I. ; Levy-Tacher, S.I. ; Boer, W.F. de; Galindo-Gonzalez, J. ; Ramirez-Marcial, N. - \ 2013
    Journal of Tropical Ecology 29 (2013)2. - ISSN 0266-4674 - p. 173 - 180.
    tropical rain-forest - species richness - costa-rica - overstory composition - abandoned pastures - growth-responses - restoration - plantations - regeneration - litter
    Species-specific traits of trees affect ecosystem dynamics, defining forest structure and understorey development. Ochroma pyramidale is a fast-growing tree species, with life-history traits that include low wood density, short-lived large leaves and a narrow open thin crown. We evaluated forest succession in O. pyramidale-dominated secondary forests, diverse secondary forests, both 10–15 y since abandonment, and rain forests by comparing height, density and basal area of all trees (> 5 cm dbh). Furthermore, we compared species richness of understorey trees and shrubs, and basal area and density of trees of early- and late-successional species (<5 cm dbh) between forest types. We found that tree basal area (mean ± SD: 32 ± 0.9 m2 ha-1) and height (12.4 ± 1.8 m) of canopy trees were higher, and density (1450 ± 339 ha-1) lower in O. pyramidale forests than in diverse forests, and more similar to rain forest. Understorey shrub diversity and tree seedling density and diversity were lower in O. pyramidale forests than in diverse forests, but these forest types had a similar density of early- and late-successional trees. Canopy openness (> 15%) and leaf litter (> 10 cm) were both highest in O. pyramidale forests, which positively affected density of understorey trees and shrubs and negatively affected density of late-successional trees. In conclusion, O. pyramidale forests presented structural features similar to those of rain forest, but this constrained the establishment of understorey tree species, especially late-successional species, decreasing successional development
    Forest management and regeneration of tree species in the Eastern Amazon
    Schwartz, G. - \ 2013
    Wageningen University. Promotor(en): Frits Mohren; Bas Arts, co-promotor(en): Marielos Pena Claros; J.C.A. Lopes. - S.l. : s.n. - ISBN 9789461734662 - 132
    bosbedrijfsvoering - bomen - soorten - verjonging - houtkap - houtteelt - amazonia - forest management - trees - species - regeneration - logging - silviculture - amazonia

    Forest management for timber production applied in the Brazilian Amazon follows a polycyclic silvicultural system where harvesting is done through reduced-impact logging (RIL). In this study the short- and medium-term effects of RIL on the regeneration of commercial tree species were assessed in the Tapajós National Forest, Eastern Amazon, Brazil. Besides, post-harvesting silvicultural techniques such as enrichment planting using commercial tree species and tending naturally established individuals in gaps created by RIL were tested in Jari Valley, Eastern Amazon, Brazil in order to improve forest management for ensuring sustainable timber production. Finally the profitability of the tested post-harvesting silvicultural treatments was evaluated. Results showed that RIL did not have a destructive effect on the regeneration of the investigated species. In the short-term RIL caused unevenly spatially distributed disturbances over the forest, which tended to increase recruitment and growth rates of seedlings and saplings in the medium-term. The silvicultural techniques proved to be efficient to decrease mortality and increase growth rates of commercial tree species but are not profitable under the current timber prices and harvesting operation costs in the Brazilian Amazon. Although not profitable, enrichment planting in logging gaps showed to be an important tool for conserving rare species.

    Tracking rodent-dispersed large seeds with Passive Integrated Transponder (PIT) tags
    Suselbeek, L. ; Jansen, P.A. ; Prins, H.H.T. ; Steele, M.A. - \ 2013
    Methods in Ecology and Evolution 4 (2013)6. - ISSN 2041-210X - p. 513 - 519.
    quercus-robur seedlings - yellow pine chipmunks - cotyledon removal - cache pilferage - identification - growth - predation - regeneration - technology - management
    1.Seed dispersal, a critical phase in the life history of many plants, is poorly understood due to the difficulty of tracking and monitoring dispersing seeds until they reach their ultimate fate. Scatter-hoarding rodents play a substantial part in the seed dispersal process of many plant species, however, existing tracking methods do not allow seed monitoring without risk of influencing the hoarding process and seed fate. 2.Here, we describe and test the use of Passive Integrated Transponders (PIT) tags inserted into seeds for the tracking and monitoring of large seeds dispersed by rodents. Unlike other tagging methods, PIT tagging combines the advantages of leaving no external cues and being readable without disturbance of caches. Rodents cannot remove these tags. 3.We evaluated the performance of PIT tagging through a series of trials with Quercus acorns dispersed by rodents, both in North America and in Europe, with equipment from different manufacturers. We quantified effects of tagging on seed removal and caching, cache pilferage and seed germination, by comparison between PIT-tagged and untagged acorns. We evaluated the detectability of buried tags to researchers. 4.Minimal effects of PIT tagging on seed removal, caching, pilferage and germination were found. Buried PIT tags were retrieved with high reliability by naïve researchers, even at burial depths up to 30 cm. Identification codes could be read even when multiple tags were buried at a single location, as in larder hoarding. 5.The method was successfully applied in two field studies of dispersal of Quercus palustris and Q. rubra acorns by Eastern grey squirrels Sciurus carolinensis in North America, and Q. robur acorns by Wood mice Apodemus sylvaticus in the Netherlands. The proportion of seeds recovered was comparable to that in studies using traditional thread tags. 6.We conclude that PIT tagging is a particularly suitable method for tracking and monitoring of seeds dispersed by scatter-hoarding rodents. PIT tagging solves most of the main problems generally encountered when following the fate of rodent-dispersed seeds over time.
    Ontwikkeling van soortensamenstelling en kwaliteit van gemengde natuurlijke bosverjonging
    Oosterbaan, A. ; Berg, C.A. van den - \ 2012
    Vakblad Natuur Bos Landschap 2012 (2012)mei. - ISSN 1572-7610 - p. 14 - 17.
    bosecologie - verjonging - bosverrijking - zandgronden - forest ecology - regeneration - improvement planting - sandy soils
    Bij gemengde verjongingen is het soms een probleem om gewenste boomsoort(en) in de menging te houden. Om een gewenste soort voldoende kans te bieden, moet wellicht in een vroeg stadium ingegrepen worden. In 2010 is een onderzoek uitgevoerd naar de ontwikkeling in de eerste 15-25 jaar van de belangrijkste gemengde natuurlijke verjongingstypen in bossen op hoge zandgronden. Hierbij is ook gekeken naar de noodzaak om in deze leeftijdsfase beheermaatregelen uit te voeren.
    Shrub facilitation increases plant diversity along an arid scrubland-temperate rainforest boundary in South America
    Zonneveld, M.J. van; Gutierrez, J.R. ; Holmgren, M. - \ 2012
    Journal of Vegetation Science 23 (2012)3. - ISSN 1100-9233 - p. 541 - 551.
    stress-gradient hypothesis - positive interactions - herbivore pressure - tree establishment - atacama desert - coastal chile - nurse plants - communities - regeneration - underneath
    Theoretical models predict nurse plant facilitation enhances species richness by ameliorating stressful environmental conditions and expanding distributional ranges of stress-intolerant species into harsh environments. We studied the role of nurse facilitation on the recruitment of perennial plants along an arid scrubland–temperate rain forest boundary to test the following predictions: (1) nurse shrub canopy increases seedling abundance and species richness along the rain forest–scrubland boundary; (2) scrubland species are less dependent on facilitative interactions than temperate rain forest species, especially at the moister, upper end of the gradient.
    Field testing and exploitation of genetically modified cassava with low-amylose or amylose-free starch in Indonesia
    Koehorst-van Putten, H.J.J. ; Sudarmonowati, E. ; Herman, M. ; Pereira-Bertram, I.J. ; Wolters, A.M.A. ; Meima, H. ; Vetten, N. de; Raemakers, C.J.J.M. ; Visser, R.G.F. - \ 2012
    Transgenic Research 21 (2012)1. - ISSN 0962-8819 - p. 39 - 50.
    manihot-esculenta crantz - cyclic somatic embryogenesis - t-dna - potato - transformation - plants - regeneration - expression - synthase - cultures
    The development and testing in the field of genetically modified -so called- orphan crops like cassava in tropical countries is still in its infancy, despite the fact that cassava is not only used for food and feed but is also an important industrial crop. As traditional breeding of cassava is difficult (allodiploid, vegetatively propagated, outbreeding species) it is an ideal crop for improvement through genetic modification. We here report on the results of production and field testing of genetically modified low-amylose transformants of commercial cassava variety Adira4 in Indonesia. Twenty four transformants were produced and selected in the Netherlands based on phenotypic and molecular analyses. Nodal cuttings of these plants were sent to Indonesia where they were grown under biosafety conditions. After two screenhouse tests 15 transformants remained for a field trial. The tuberous root yield of 10 transformants was not significantly different from the control. Starch from transformants in which amylose was very low or absent showed all physical and rheological properties as expected from amylose-free cassava starch. The improved functionality of the starch was shown for an adipate acetate starch which was made into a tomato sauce. This is the first account of a field trial with transgenic cassava which shows that by using genetic modification it is possible to obtain low-amylose cassava plants with commercial potential with good root yield and starch quality.
    Ungulate herbivory modifies the effects of climate change on mountain forests
    Didion, M.P. ; Kupferschmid, A.D. ; Wolf, A. ; Bugmann, H. - \ 2011
    Climatic Change 109 (2011)3-4. - ISSN 0165-0009 - p. 647 - 669.
    white-tailed deer - gap model - species composition - treeline position - inventory data - european alps - swiss alps - responses - regeneration - dynamics
    Recent temperature observations suggest a general warming trend that may be causing the range of tree species to shift to higher latitudes and altitudes. Since biotic interactions such as herbivory can change tree species composition, it is important to understand their contribution to vegetation changes triggered by climate change. To investigate the response of forests to climate change and herbivory by wild ungulates, we used the forest gap model ForClim v2.9.6 and simulated forest development in three climatically different valleys in the Swiss Alps. We used altitudinal transects on contrasting slopes covering a wide range of forest types from the cold (upper) to the dry (lower) treeline. This allowed us to investigate (1) altitudinal range shifts in response to climate change, (2) the consequences for tree species composition, and (3) the combined effect of climate change and ungulate herbivory. We found that ungulate herbivory changed species composition and that both basal area and stem numbers decreased with increasing herbivory intensity. Tree species responded differently to the change in climate, and their ranges did not change concurrently, thus causing a succession to new stand types. While climate change partially compensated for the reductions in basal area caused by ungulate herbivory, the combined effect of these two agents on the mix of the dominant species and forest type was non-compensatory, as browsing selectively excluded species from establishing or reaching dominance and altered competition patterns, particularly for light. We conclude that there is an urgent need for adaptive forest management strategies that address the joint effects of climate change and ungulate herbivory.
    Growth response of Pterocarpus soyauxii and Lophira alata seedlings to host soil mycorrhizal inocula in relation to land use types.
    Onguene, N.A. ; Ngonkeu, L.E.M. ; Kuyper, T.W. - \ 2011
    African Journal of Microbiology Research 5 (2011)17. - ISSN 1996-0808 - p. 2391 - 2398.
    rain-forest - arbuscular mycorrhizae - tropical forest - south cameroon - plant-growth - fungi - colonization - regeneration - communities
    Deficiency in mycorrhizal inoculum in soils due to land use types (LUT) can be alleviated by quantity and quality inoculum addition. A bioassay was carried out to determine how host soil mycorrhizal inoculum influenced mycorrhizal colonization, carbon allocation and partitioning of seedlings of two native timber species of Cameroon humid forest. Seedlings of Pterocarpus soyauxii and Lophira alata were raised for six months on surface soils (0 - 20 cm) collected from early secondary forests and LUT derived from slash-and-burn agriculture and selective logging. Mycorrhizal inoculation effect (MIE) was derived. Seedlings were mainly colonized by members of the Glomaceae and Gigasporaceae, respectively, as shown by molecular typing. They generally performed poorly in soils with indigenous inoculum. But addition of soil inoculum from P. soyauxii trees favored nodulation, significantly increased mycorrhizal colonization and total biomass but decreased root-to-shoot ratios, resulting in large and positive MIE, irrespective of LUT. ln contrast, host soil inoculum of L. alata did not affect fractional mycorrhizal colonization but significantly increased total biomass and resulted in high carbon allocation to roots in low and sometimes negative MIE. Therefore, seedlings' responses to mycorrhizal inoculum depend on host soil inoculum and that could be critical for successful rejuvenation of tropical trees.
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