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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    Fungal artillery of zombie flies: infectious spore dispersal using a soft water cannon
    Ruiter, Jolet de; Arnbjerg-Nielsen, Sif Fink ; Herren, Pascal ; Høier, Freja ; Fine Licht, Henrik H. De; Jensen, Kaare H. - \ 2019
    Journal of the Royal Society, Interface 16 (2019)159. - ISSN 1742-5689 - 10 p.
    biomimetic soft cannon - dispersal range - Entomophthora muscae - force-balance model - fungal spore ejection - high-speed videography

    Dead sporulating female fly cadavers infected by the house fly-pathogenic fungus Entomophthora muscae are attractive to healthy male flies, which by their physical inspection may mechanically trigger spore release and by their movement create whirlwind airflows that covers them in infectious conidia. The fungal artillery of E. muscae protrudes outward from the fly cadaver, and consists of a plethora of micrometric stalks that each uses a liquid-based turgor pressure build-up to eject a jet of protoplasm and the initially attached spore. The biophysical processes that regulate the release and range of spores, however, are unknown. To study the physics of ejection, we design a biomimetic 'soft cannon' that consists of a millimetric elastomeric barrel filled with fluid and plugged with a projectile. We precisely control the maximum pressure leading up to the ejection, and study the cannon efficiency as a function of its geometry and wall elasticity. In particular, we predict that ejection velocity decreases with spore size. The calculated flight trajectories under aerodynamic drag predict that the minimum spore size required to traverse a quiescent layer of a few millimetres around the fly cadaver is approximately 10 µm. This corroborates with the natural size of E. muscae conidia (approx. 27 µm) being large enough to traverse the boundary layer but small enough (less than 40 µm) to be lifted by air currents. Based on this understanding, we show how the fungal spores are able to reach a new host.

    Reviewing the taxonomy of Podaxis : Opportunities for understanding extreme fungal lifestyles
    Conlon, Benjamin H. ; Aanen, Duur K. ; Beemelmanns, Christine ; Beer, Z.W. de; Fine Licht, Henrik H. De; Gunde-Cimerman, Nina ; Schiøtt, Morten ; Poulsen, Michael - \ 2019
    Fungal Biology 123 (2019)3. - ISSN 1878-6146 - p. 183 - 187.
    Basidiomycota - Drought - Extremophile - Low water activity - Termite

    There are few environments more hostile and species-poor than deserts and the mounds of Nasutitermitinae termites. However, despite the very different adaptations required to survive in such extreme and different environments, the fungal genus Podaxis is capable of surviving in both: where few other fungi are reported to grow. Despite their prominence in the landscape and their frequent documentation by early explorers, there has been relatively little research into the genus. Originally described by Linnaeus in 1771, in the early 20th Century, the then ∼25 species of Podaxis were almost entirely reduced into one species: Podaxis pistillaris. Since this reduction, several new species of Podaxis have been described but without consideration of older descriptions. This has resulted in 44 recognised species names in Index Fungorum but the vast majority of studies and fungarium specimens still refer to P. pistillaris. Studies of Podaxis' extremely different lifestyles is hampered by its effective reduction to a single-species genus. Here we examine the history of the taxonomy of Podaxis before focusing on its extreme lifestyles. From this, we consider how the muddled taxonomy of Podaxis may be resolved; opening up further avenues for future research into this enigmatic fungal genus.

    Searching for Podaxis on the trails of early explorers in southern Africa
    Buys, M. ; Conlon, B. ; Fine Licht, Henrik H. De; Aanen, D.K. ; Poulsen, M. ; Beer, Z.W. de - \ 2018
    South African Journal of Botany 115 (2018). - ISSN 0254-6299 - p. 317 - 317.
    Podaxis pistillaris is the name often given to the torpedo-shaped mushrooms forming on termite mounds across southern Africa during the rainy season. Linnaeus described the species in 1871 based on a specimen from India. In 1881, he described a second species as Lycoperdon carcinomale from a South African specimen he received from Thunberg. In 1812, Burchell made a painting of the fungus during his exploration of southern Africa. In 1933, all 33 Podaxis species described by that time from Africa, Asia, Australia and the USA, were lumped as synonyms of P. pistillaris. Another 12 species were subsequently described, but most authors treated all these fungi as P. pistillaris. In a quest to resolve the taxonomy of the fungus, we studied Southern African specimens from various herbaria, and some specimens from the USA, Mexico, India, and Africa. We also visited the sites where Thunberg collected his specimen (Western Cape) and where Burchell made his painting (Northern Cape), but could not find fresh specimens. We distributed flyers to local communities in these areas and requested that they contact us should Podaxis be observed. Within six weeks we received specimens from a farm close to Burchell’s camp site, and more from the Northern and Eastern Cape. Ribosomal DNA sequences were successfully obtained from all the fresh and almost all herbarium specimens, including some older than 100 years. Phylogenetic analyses showed that the southern African specimens separate in at least five distinct species, some of which might represent novel taxa
    Tuning for light and more : engineering phototrophy and membrane proteins in Escherichia coli
    Claassens, Nicolaas J.H.P. - \ 2017
    Wageningen University. Promotor(en): John van der Oost; Willem de Vos, co-promotor(en): Vitor Martins dos Santos. - Wageningen : Wageningen University - ISBN 9789463430920 - 328
    escherichia coli - phototropism - membranes - proteins - light - photosystem i - gene expression - escherichia coli - fototropie - membranen - eiwitten - licht - fotosysteem i - genexpressie

    The application of microbial and plant photosynthesis for biobased production on the one hand has a huge potential but on the other hand photosynthesis has serious limitations regarding its efficiency. Hence, studying both fundamental features of photosynthetic processes and engineering of photosystems is of paramount interest, exploring the engineering of photosystems is the overarching aim of this thesis. As described in Chapter 1, natural photosystems may be modified or transplanted to allow for more efficient conversion of solar light energy into biochemical energy. Hereto ambitious proposals to engineer photosystems have been made, and to realize those endeavors the disciplines of synthetic and systems biology are required. To explore how to apply and improve those disciplines hereto, the work described in this thesis has focused on the transplantation of simple photosystems (proton-pumping rhodopsins; PPRs) into the cell membrane of the heterotrophic model bacterium Escherichia coli. Both in silico analyses, including metabolic and thermodynamic modeling (Chapter 3) and a series of experimental studies on transplanting PPR photosystems (Chapters 4,6 and 7) were performed, which identified several challenges, limitations and most importantly opportunities. This thesis also describes the application of novel tools to substantially improve the functional production of PPRs and a variety of other membrane proteins in E. coli.

    Chapter 2 provides more details on previously reported examples of heterologous expression of PPRs in several hosts, and on the physiological impact of these transplanted photosystems. Based on this evaluation, some suggestions are made to improve and further exploit the transplantation of these photosystems.

    In Chapter 3 a systematic, integrated in silico analysis is made of anaerobic, photo-electro-autotrophic synthetic metabolism in E. coli, consisting of (i) a PPR photosystem for ATP regeneration, (ii) an electron uptake pathway, and (iii) a natural or synthetic carbon fixation pathway. Constraint-based metabolic modelling of E. coli central metabolism is used, in combination with kinetic and thermodynamic pathway analyses. The photo-electro-autotrophic designs are predicted to have a limited potential for anaerobic, autotrophic growth of E. coli, given the relatively low ATP regenerating capacity of the PPR photosystems, and the relatively high ATP consumption due to maintenance. In general these analyses illustrate the potential of in silico analyses to identify potential bottlenecks and solutions in complex designs for autotrophic and photosynthetic metabolism, as a basis for subsequent experimental implementation.

    To tackle a main bottleneck of PPR systems: their functional membrane-embedded production level, the heterologous production in E. coli of the proton-pumping rhodopsins from Gloeobacter violaceus (GR) and from Thermus thermophilus JL18 (TR) is quantified and experimentally optimized in Chapter 4. High constitutive production of both rhodopsin proteins is achieved by fine-tuning transcription and translation. Besides the canonical retinal pigment, the GR system has the ability to bind a light-harvesting antennae pigment, echinenone. After optimization of the heterologous pigment biosynthesis pathways for either retinal or echinenone production, appropriate quantities of retinal or echinenone for PPR reconstitution were detected in E. coli. Association of echinenone with GR broadens its absorption spectrum in E. coli, broadening the potential for light-harvesting also to blue light. Optimization of the branched pathway for simultaneous biosynthesis of both retinal and echinenone has been attempted by using a smart library of variable Ribosome Binding Sites (RBSs) with varying strengths (RedLibs). In general, the here described approaches towards improved functional production of rhodopsin photosystems in E. coli and their pigments may prove more widely applicable for heterologous production of more complex photosystems and other systems.

    In Chapter 5 an up-to-date overview is provided on how codon usage can influence functional protein production. The fact that all known organisms have an incomplete set of tRNAs, indicates that biased codon usage could act as a general mechanism that allows for fine-tuning the translation speed. Although translation initiation is the key control step in protein production, it is broadly accepted that codon bias, especially in regions further downstream of the start codon, can contribute to the translation efficiency by tuning the translation elongation rate. Modulation of the translation speed depends on a combination of factors, including the secondary structure of the transcript (more or less RNA hairpins), the codon usage landscape (frequent and more rare codons) and for bacteria also RBS-like sequences at which ribosomes can pause. The complex combination of interdependent factors related to codon usage that can influence translation initiation and elongation. This complexity makes that the design of synthetic genes for heterologous expression is still in its infancy, and despite the availability of some codon usage algorithms, it is often as well a matter of trial and error.

    In Chapter 6 the effect of different codon usage algorithms (optimization and harmonization) has been experimentally tested for heterologous production of membrane proteins. Apart from the codon usage algorithms also the combined effect of transcriptional fine-tuning in E. coli LEMO21(DE3) was assessed. The overproduction of 6 different membrane-embedded proteins, including 4 PPR variants (from bacteria, archaea and eukaryotes), was tested. For production of tested PPR variants, the different codon usage algorithms hardly influenced production, while transcriptional tuning had a large impact on production levels. Interestingly, for the other two tested non-PPR membrane proteins, some codon usage variants significantly improved production on top of transcriptional tuning. For both these proteins the codon-optimization algorithm reduced functional production below that of the wild-type codon variant, while the harmonization algorithm gave significantly higher production, equal or even higher than for the wild-type variant.

    In Chapter 7 it is demonstrated that a translational-tuning system can be used to successfully optimize the expression of several membrane proteins, based on initial findings presented in Chapter 4. The employed, recently developed Bicistronic Design (BCD) system is based on translational coupling of a gene encoding a short leader peptide and the gene of interest that is under control of a variable ribosome binding site. A standardized library of 22 RBSs allows for precise, gene context-independent, fine-tuning of expression of this second gene, here encoding a membrane protein. For all four membrane proteins tested in this study the BCD approach resulted in 3 to 7-fold higher protein levels than those obtained by two other recently developed methods for optimizing membrane protein production. The presented approach allows for inducer-free, constitutive, high-level production of membrane proteins in E. coli, which can be widely applicable for both membrane protein purification studies as well as for synthetic biology projects involving membrane proteins.

    In Chapter 8 a broad review and perspectives are provided on the potential of microbial autotrophs for the production of value-added compounds from CO2. Both photoautotrophic and chemolithoautotrophic production platforms are discussed, and recent progress in improving their efficiency and production potential is highlighted. Transplantation efforts for photosystems, but also for CO2 fixation pathways and electron uptake systems are discussed. An overview is provided on novel in silico and experimental approaches to engineer components related to autotrophy in heterotrophic and autotrophic model hosts, including approaches applied in this thesis. Future avenues are discussed for realizing more efficient autotrophic production platforms.

    Finally, in Chapter 9 and 10 the work in this thesis is summarized and a general discussion is provided on future avenues for engineering of PPR photosystems, photosystems in general and on the optimization of membrane protein production.

    Phylogenetic analyses of Podaxis specimens from Southern Africa reveal hidden diversity and new insights into associations with termites
    Conlon, Benjamin H. ; Beer, Z.W. de; Fine Licht, Henrik H. De; Aanen, Duur K. ; Poulsen, Michael - \ 2016
    Fungal Biology 120 (2016)9. - ISSN 1878-6146 - p. 1065 - 1076.
    Herbarium - Namibia - Nasutitermitinae - South Africa - Trinervitermes

    Although frequently found on mounds of the grass-cutting termite genus . Trinervitermes, virtually nothing is known about the natural history of the fungal genus . Podaxis (Agaricaceae) nor why it associates with termite mounds. More than 40 species of this secotioid genus have been described since Linnaeus characterised the first species in 1771. However, taxonomic confusion arose when most of these species were reduced to synonymy with . Podaxis pistillaris in 1933. Although a few more species have since been described, the vast majority of specimens worldwide are still treated as . P. pistillaris. Using 45 fresh and herbarium specimens from Southern Africa, four from North America and one each from Ethiopia, and Kenya, we constructed the first comprehensive phylogeny of the genus. Four of the genotyped specimens were more than 100 y old. With the exception of the type specimen of . Podaxis rugospora, all herbarium specimens were labelled as . P. pistillaris or . Podaxis sp. However, our data shows that the genus contains at least five well-supported clades with significant inter-clade differences in spore length, width and wall thickness, and fruiting body length, supporting that clades likely represent distinct . Podaxis species. Certain clades consistently associate with termites while others appear entirely free-living.

    Light harvesting, light adaptation and photoprotection in aquatic photosynthesis studies by time-resolved fluorescence spectroscopy
    Chukhutsina, V. - \ 2015
    Wageningen University. Promotor(en): Herbert van Amerongen. - Wageningen : Wageningen University - ISBN 9789462572454 - 190
    licht - adaptatie - bacillariophyta - cyanobacteriën - verdedigingsmechanismen - fotochemie - spectrofluorimetrie - light harvesting complexen - light - adaptation - bacillariophyta - cyanobacteria - defence mechanisms - photochemistry - spectrofluorimetry - light harvesting complexes

    Summary

    Aquatic photosynthetic organisms unavoidably experience light fluctuations that vary in amplitude, duration and origin, compromising their photosynthetic efficiency. Weather conditions and underwater flow cause continuous changes in irradiance to which the organisms have to adapt. Many light-adaptation strategies of photosynthetic organisms, such as light acclimation, photoprotection and state transitions are still not well understood. In this thesis, time-resolved fluorescence spectroscopy is used to obtain insight into the response of diatoms and cyanobacteria, both aquatic photosynthetic organisms, to changing light conditions.

    In chapter 2, photoacclimation (long-term acclimation to irradiance conditions) of the diatom Cyclotella meneghiniana is discussed. It is shown that the diatom cells fine-tune the amount of absorbed light energy by modifying their antenna size: cells grown in high light intensity have smaller antennas than those grown in low light. At the same time, the increase of growth light intensity leads to a decrease of the relative amount of photosystem I (PSI) as compared to PSII. Such a strategy might be beneficial for diatoms, since they are known to have an electron transfer cycle around PS II to release excess electrons produced in high light intensities. Besides discussing photoacclimation, we give a detailed description the fluorescence kinetics in C. meneghiniana. It is concluded that the diatom antenna, represented by light-harvesting fucoxanthin chlorophyll proteins (FCPs), transfer their excitation energy predominantly to PSII. FCPs associated with PSII are slightly richer in red-absorbing fucoxanthin than the FCPs associated with PSI, suggesting that PSII antennas (partly) constitute the antenna form FCPb (i.e. oligomeric antenna complexes).

    In chapter 3 the process of non-photochemical quenching (NPQ, thermal dissipation of excess absorbed light energy) of chlorophyll a fluorescence was studied in the same diatom species. Diatoms can rapidly switch on/off NPQ to respond to fast light-intensity changes in moving waters. They are capable to induce higher NPQ values than plants or other photosynthetic organisms. The reason for such high NPQ values, however, is not clear. We performed picosecond fluorescence measurements at 77K on cells locked in three different states: Besides using conventional unquenched and quenched states of the cells (in the absence and presence of the total NPQ component, respectively), we also performed measurements on the dark-adapted state directly following NPQ. In this state, diatoxantin (Dtx, a carotenoid related to NPQ), accumulated during the NPQ period and Dtx-related NPQ persists, while ΔpH-related NPQ has relaxed. In this way we revealed the following sequence of events during full development of NPQ. First, the pH gradient across the thylakoid membrane induces quenching of FCP trimers (FCPa complexes), while they are still part of PSII. This is followed by (partial) detachment of FCPa from PSII after which quenching persists. The pH gradient also causes the formation of Dtx, which leads to further quenching of isolated PSII cores and some aggregated FCPa. To summarize, quenching of PSII -both cores and complexes- and FCPa substantially contribute to NPQ in diatoms. The FCPb antenna form on the other hand does not contribute to the NPQ process.

    Certain aquatic photosynthetic organisms, such as cyanobacteria and green algae, can also cope with changing light conditions by dynamically varying the relative antenna size of PSI and of PSII. Consequently, a redistribution of light energy between the PSs is achieved. This phenomenon is called “state transitions”. It is known to be driven via a change in the redox status of electron carriers between PSII and PSI. In cyanobacteria, this redox change can be achieved via dark-light transitions. However, the cascade of microscopic events that lead to subsequent energy redistribution in cyanobacteria is still not completely clear. In chapter 4, a study on dark-light transitions using the cyanobacterium Synechocystis sp. PCC 6803 as a model organism is described. It is demonstrated that during dark to light transitions, there is mainly detachment of phycobilisomes (PBSs) (cyanobacterial antennas) from PSI, generally not followed by their attachment to PSII: only 15 % of the PBSs that detach from PSI actually move to PSII, while the major part remains detached from both PSs. We conclude that PSI-PSII-PBS megacomplexes, which were recently isolated using chemical cross-linking, are not involved in dark/light state transitions, suggesting that, if present, they are only transiently formed in cyanobacteria. To summarize, the findings presented in chapter 4 suggest that in cyanobacteria, unlike in green algae or higher plants, the main role of state transitions is to change the absorption cross-section of PSI, rather than that of PSII.

    In chapter 5, a study of the role of flv4-2 operon-encoded proteins in Synechocystis is described. Three genes are found in the operon: Flv4, Sll0218, and Flv2. Only recently flv4-2 operon-encoded proteins were found to constitute an additional photoprotective mechanism in a number of cyanobacteria by safeguarding PSII activity via an alternative electron chain. Its contribution becomes vital for the cells in high light and in air-level CO2, when the photosynthetic electron transport chain is over-reduced. It is demonstrated that deletion of the operon induces 20% PBS detachment. The reduced PSII dimer to monomer ratio, as a result of the absence of the small Sll0218 protein, favors a relative decrease of the PSII dimer content of about 20%, showing a direct correlation between PSII dimer destabilization and PBS detachment from reaction centers. On the other hand, the suggested binding of the Flv2/Flv4 heterodimer closely to the quinone B (QB) pocket in PSII increases the QB redox potential, thereby promoting forward electron transfer and increasing the charge separation rates in PSII. This activity of the Flv2/Flv4 heterodimer in combination with its earlier reported role as an electron acceptor in alternative electron chain provides more oxidized state of the PQ pool in high light and in air-level CO2.

    Meer proeven nodig om effect van hogere F-scatterwaarde te achterhalen : diffuus glas komt in de fase van fine-tuning (interview met Silke Hemming en Tom Dueck)
    Kierkels, T. ; Hemming, S. ; Dueck, T.A. - \ 2014
    Onder Glas 11 (2014)6/7. - p. 40 - 41.
    glastuinbouw - diffuus glas - lichtdoorlating - verstrooiing - kwaliteit - groei - kastechniek - greenhouse horticulture - diffused glass - light transmission - scattering - quality - growth - greenhouse technology
    Diffuus glas is over vijftien jaar de standaard. Wie nu nieuw bouwt, heeft veel goede redenen om voor diffuus te kiezen en vrijwel geen om het te laten, zeggen Silke Hemming en Tom Dueck van Wageningen UR Glastuinbouw. De inzichten in het nut van diffuus licht én de technische ontwikkelingen schrijden nog elk jaar voort. Een update.
    Maatregelen ter vermindering van fijnstofemissie uit de pluimveehouderij : verkenning effecten alternatieve lichtschema's op fijnstofemissie bij leghennen = Measures to reduce fine dust from poultry houses : investigation of the effects of light regimes on fine dust in layer houses
    Emous, R.A. van; Ogink, N. - \ 2010
    Lelystad : Wageningen UR Livestock Research (Rapport / Wageningen UR Livestock Research 347) - 11
    dierenwelzijn - luchtkwaliteit - pluimveehouderij - hennen - fijn stof - emissie - licht - kunstmatige verlichting - animal welfare - air quality - poultry farming - hens - particulate matter - emission - light - artificial lighting
    Light intensity has a large effect on the activity of laying hens. A lower intensity gives less activity and thus less emission of fine dust. The effect on the welfare of hens is difficult to estimate.
    igh Symbiont Relatedness Stabilizes Mutualistic Cooperation in Fungus-Growing Termites
    Aanen, D.K. ; Fine Licht, H.H. De; Debets, A.J.M. ; Kerstes, N.A.G. ; Hoekstra, R.F. ; Boomsma, J.J. - \ 2009
    Science 326 (2009)5956. - ISSN 0036-8075 - p. 1103 - 1106.
    macrotermes-natalensis - evolution - termitomyces - agriculture - isoptera - host - ants - incompatibility - transmission - conflict
    It is unclear how mutualistic relationships can be stable when partners disperse freely and have the possibility of forming associations with many alternative genotypes. Theory predicts that high symbiont relatedness should resolve this problem, but the mechanisms to enforce this have rarely been studied. We show that African fungus-growing termites propagate single variants of their Termitomyces symbiont, despite initiating cultures from genetically variable spores from the habitat. High inoculation density in the substrate followed by fusion among clonally related mycelia enhances the efficiency of spore production in proportion to strain frequency. This positive reinforcement results in an exclusive lifetime association of each host colony with a single fungal symbiont and hinders the evolution of cheating. Our findings explain why vertical symbiont transmission in fungus-growing termites is rare and evolutionarily derived
    Asymmetric interaction specificity between two sympatric termites and their fungal symbionts.
    Fine Licht, H.H. De; Boomsma, J.J. - \ 2007
    Ecological Entomology 32 (2007)1. - ISSN 0307-6946 - p. 76 - 81.
    growing termites - termitomyces sp - macrotermes-natalensis - lignin degradation - isoptera - digestion - origin - transmission - purification - polyethism
    1. Fungus-growing termites live in an obligate mutualistic symbiosis with Termitomyces fungi. The functions of the fungal symbiont have been hypothesised to differ between species and to range from highly specific roles of providing plant-degrading enzymes complementary to termite gut enzymes, to non-specific roles of providing protein-rich food to the termites. 2. Termite species with unspecialised fungal symbionts are predicted to be associated with a wider range of symbionts than species with specialised symbionts. Recent DNA data have confirmed this prediction, but evidence for differences in functional specificity has been sparse and indirect. 3. Here the consequences of symbiont interaction specificity are experimentally tested by reciprocally exchanging the fungal symbionts of sympatric colonies of Macrotermes natalensis and Odontotermes badius, which were inferred to have specialised and non-specialised symbionts respectively. 4. As expected, survival of O. badius termites on M. natalensis fungus was not significantly worse than on their own fungus, but survival of M. natalensis termites on O. badius fungus was significantly reduced. 5. This asymmetric result confirms that symbiont roles differ significantly between macrotermitine genera and indicates that symbiont transplantation experiments are a powerful tool for testing the functional details of mutualistic symbioses.
    Patterns of interaction specificity of fungus-growing termites and Termitomyces symbionts in South Africa
    Aanen, D.K. ; Ros, V.I.D. ; Fine Licht, H.H. de; Mitchell, J. ; Beer, Z.W. de; Slippers, B. ; Rouland-Lefevre, C. ; Boomsma, J.J. - \ 2007
    BMC Evolutionary Biology 7 (2007). - ISSN 1471-2148 - 11 p.
    multiple sequence alignment - phylogenetic-relationships - evolutionary history - ants - macrotermitinae - isoptera - colonies - models - trees - comb
    Background Termites of the subfamily Macrotermitinae live in a mutualistic symbiosis with basidiomycete fungi of the genus Termitomyces. Here, we explored interaction specificity in fungus-growing termites using samples from 101 colonies in South-Africa and Senegal, belonging to eight species divided over three genera. Knowledge of interaction specificity is important to test the hypothesis that inhabitants (symbionts) are taxonomically less diverse than 'exhabitants' (hosts) and to test the hypothesis that transmission mode is an important determinant for interaction specificity. Results Analysis of Molecular Variance among symbiont ITS sequences across termite hosts at three hierarchical levels showed that 47 % of the variation occurred between genera, 18 % between species, and the remaining 35 % between colonies within species. Different patterns of specificity were evident. High mutual specificity was found for the single Macrotermes species studied, as M. natalensis was associated with a single unique fungal haplotype. The three species of the genus Odontotermes showed low symbiont specificity: they were all associated with a genetically diverse set of fungal symbionts, but their fungal symbionts showed some host specificity, as none of the fungal haplotypes were shared between the studied Odontotermes species. Finally, bilaterally low specificity was found for the four tentatively recognized species of the genus Microtermes, which shared and apparently freely exchanged a common pool of divergent fungal symbionts. Conclusion Interaction specificity was high at the genus level and generally much lower at the species level. A comparison of the observed diversity among fungal symbionts with the diversity among termite hosts, indicated that the fungal symbiont does not follow the general pattern of an endosymbiont, as we found either similar diversity at both sides or higher diversity in the symbiont. Our results further challenge the hypothesis that transmission-mode is a general key-determinant of interaction specificity in fungus-growing termites.
    Presumptive horizontal symbiont transmission in the fungus-growing termite Macrotermes natalensis
    Fine Licht, H.H. de; Boomsma, J.J. ; Aanen, D.K. - \ 2006
    Molecular Ecology 15 (2006)11. - ISSN 0962-1083 - p. 3131 - 3138.
    odontotermes-formosanus - phylogenetic inference - population-genetics - isoptera - recombination - comb - sequences - colonies - basidiomycota - establishment
    All colonies of the fungus-growing termite Macrotermes natalensis studied so far are associated with a single genetically variable lineage of Termitomyces symbionts. Such limited genetic variation of symbionts and the absence of sexual fruiting bodies (mushrooms) on M. natalensis mounds would be compatible with clonal vertical transmission, as is known to occur in Macrotermes bellicosus. We investigated this hypothesis by analysing DNA sequence polymorphisms as codominant SNP markers of four single-copy gene fragments of Termitomyces isolates from 31 colonies of M. natalensis. A signature of free recombination was found, indicative of frequent sexual horizontal transmission. First, all 31 strains had unique multilocus genotypes. Second, SNP markers (n = 55) were largely in Hardy-Weinberg equilibrium (90.9%) and almost all possible pairs of SNPs between genetically unlinked loci were in linkage equilibrium (96.7%). Finally, extensive intragenic recombination was found, especially in the EF1 alpha fragment. Substantial genetic variation and a freely recombining population structure can only be explained by frequent horizontal and sexual transmission of Termitomyces. The apparent variation in symbiont transmission mode among Macrotermes species implies that vertical symbiont transmission can evolve rapidly. The unexpected finding of horizontal transmission makes the apparent absence of Termitomyces mushrooms on M. natalensis mounds puzzling. To our knowledge, this is the first detailed study of the genetic population structure of a single lineage of Termitomyces.
    Trees and light : tree development and morphology in relation to light availability in a tropical rain forest in French Guiana
    Sterck, F.J. - \ 1997
    Agricultural University. Promotor(en): H.H.T. Prins; F.J.J.M. Bongers. - S.l. : Sterck - ISBN 9789054856733 - 122
    bosbouw - habitus - levensvorm - plantenontwikkeling - plantenecologie - licht - plantenmorfologie - tropische regenbossen - vegetatie - tropen - frans-guyana - natuurlijke opstanden - forestry - habit - life form - plant development - plant ecology - light - plant morphology - tropical rain forests - vegetation - tropics - french guiana - natural stands

    Tropical rain forest trees spend their life in a heterogeneous light environment. During their life history, they may change their growth in relation to different levels of light availability. Some of their physiological processes (e.g. photosynthesis, carbon allocation, and meristern activity) change with light availability, and tune their development and morphology to the ambient light levels. The underlying physiological processes are not investigated in the present study. The focus is on the development and morphology of trees of canopy species in relation to the light availability in tropical rain forest. The possible consequences for survival, growth, and reproduction of trees are not assessed directly, but are discussed on a speculative basis.

    The relationships between the light environment, tree development, and morphology are investigated for trees of different size, ranging from small saplings to trees of adult stage. Trees of increasing size are compared in order to explore the changes in tree development and morphology, and their relation to the light environment, with ontogeny. Ontogeny is referred to as the overall growth and development pattern during tree life, both for individual trees and (in more general) for a given tree species.

    The field work for this thesis was carried out in French Guiana. This country in the north-east of South America has an area of 83.000 km 2and is covered by evergreen tropical rain forest. The field work was conducted at two biological stations. 'The Piste St. Elie' station is located 30 km from the coast, south of the town of Sinnamary, and the biological station 'Les Nouragues' is located 100 km from the coast, south of Cayenne. Two canopy tree species were selected for this study: Dicorynia guianensis Amshoff. (Caesalpiniaceae) and Vouacapoua americana Aubl. (Caesalpiniaceae). Both are common species in the forests of French Guiana, and are considered late successionals or shadetolerant species (Schulz 1960). In some chapters, these species are compared with an early successional (light demanding) species, Goupia glabra Aubl. (Celastraceae). Trees of these three species are harvested for their timber in French Guiana and its surrounding countries.

    The trees that were shorter than 20 rn had not yet reached the open upper canopy. These trees usually occur at relatively low light levels. Although these trees may differ in height (from 0 to 20 m), they usually show the same type of growth response to ambient light levels. They produced more growth units and more leaves at higher light availability. They thus increased their total leaf area and leaf area index (LAI, a measure for the number of leaf layers in the crown) as a response to higher light levels. Under persisting high light levels, the increase in total leaf area may enable these trees to fix more carbohydrates (i.e. carbon) for successful growth and survival in the future. Trees with a high LAI at higher light availability, in combination with more columnar shaped crowns, achieve net photosynthesis (more carbon intake than consumption by leaves) at the least possible cost for leaf area support. In contrast, trees with more planar crowns and lower LAI at lower light availability may avoid self-shading of leaves, but risk higher costs for leaf area support.

    Trees also produced shorter growth units at lower light availability, and thus spaced their leaves at shorter distances than trees at higher light availability. In more closely spaced leaves, the investments for the support of one leaf are lower. As leaf size did not change in relation to light availability, trees displayed their leaf area more economically (at lower carbon costs) at lower light availability. In this way, they increased light interception per unit of fixed carbon, and they may thus be better able to survive the shade.

    Dicorynia and Vouacapoua trees also grew faster in height with increasing light availability. In general, trees may reduce their height growth because low light levels simply limit growth. At low light levels, trees are shaded by taller neighbouring trees which intercept the majority of light above them, but they may survive for some time by producing their leaf area slowly and efficiently. When light levels increase because one (or more) of the taller neighbours falls down, trees start to increase their height growth, and may compete with their neighbours for newly available light and space. For both species studied, it was shown that height growth further increased at very high light levels in large gaps through preferential growth of the leader (axis which supports the uppermost apical meristern of the crown) over the other axes in the crown. At lower light levels, individuals did not show preferential growth of the leader. Thus, height growth increased not only because the higher light levels are less growth limiting, but also because of preferential growth of the leader.

    These growth responses to light refer to trees (up to 20 m tall) that were still heading for the canopy. The taller trees (heights of sampled trees range between 26 and 37 m) at higher light availability in the upper canopy had a larger total leaf area and total branch length than the trees shorter than 20 m. These taller trees also produced larger and more planar shaped crowns, did not further increase their LAI, and decreased their leader growth and the space between leaves, as compared with the smaller individuals. The shift to a wider crown is probably caused by increasing light (and space) availability, and may constrain a further increase in the LAI (the leaves occurred over a much larger horizontal area). The lower leader growth and the production of leaves at shorter distances indicate that these taller trees changed from investments in vertical expansion to investments in the replacement of leaves (and flowers).

    The increasing stature with ontogeny has to be balanced by mechanical strength (thickness). This strength is needed to carry the increasing tree weight and to resist wind stress. The mechanical design expresses the balance between overall tree stature (in terms of weight or wind force experienced by the tree) and tree (mechanical) strength. The changes in mechanical design with ontogeny were investigated for Goupia, Dicorynia, and Vouacapoua using two models. (1) The elastic-stability model emphasises the mechanical strength against its own weight. Using this model, it was shown that trees of the study species decreased their 'safety margins' (strength) early in ontogeny, but increased their margins of safety later. Trees had their lowest margins at a stem diameter of 15 to 25 em. These margins were close to the theoretical minimum, i.e. trees would buckle under their own weight if they were slightly more slenderly built (taller at a given diameter). In comparison with some temperate tree species, the trees of the present study appeared to have lower safety margins because they were more slender. Slenderness (height/diameter ratio), however, is only one of the factors determining the strength of a tree. The denser and stiffer wood of tropical trees may increase the mechanical strength of tropical trees in comparison with temperate trees. Another explanation for the lower safety margins of tropical trees is that they are exposed to lower external stress forms than temperate trees. Temperate trees experience heavy storms and snow loads during their life, whereas the trees of the present study do not experience such forms of stress. (2) The constant-stress model emphasises the mechanical strength over wind stress on the tree. For the species of study, it was shown that the safety margins against wind stress increased with ontogeny. This was in line with the expectations, because wind stress is likely to increase with increasing tree stature. Finally, the influence of light availability on mechanical tree design could not be investigated. The trees studied had long life-histories under unknown light conditions, and therefore did not show a significant response within the 2-3 years of investigation.

    The ecological knowledge on commercial tree species presented in this work is thought to be useful for the fine tuning and improvement of forest management systems. In these systems, canopy gaps of different size are created, and they may affect the growth of trees. The results of this thesis indicate that manipulations of light availability (either by killing dominant trees thus inducing light level increase, or by shading) in forests may increase the timber production in trees. Besides this, the follow-up to this study may provi de morphological traits that can be used to indicate the growth potential of trees in relation to the light environment. It is suggested that there is a need for knowledge on the growth response of trees (both in terms of timber production, morphology and development) to the whole range of light availability. Manipulations of the light environment may then be tuned to individual trees of commercial species in order to approach the light conditions that provoke the desired growth response. In general, fundamental research on tree growth in a natural habitat, extended by research on tree growth at higher light levels outside the natural habitat, may provide valuable insights for the improvement of forest management systems.

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