Droevendaalsesteeg 10
6708 PB Wageningen
The Netherlands
Tanja Bakx-Schotman
About
My name is Tanja Bakx-Schotman. Molecular research assistant from TE.
Lab manager for the molecular Laboratory
Biological Safety Officer and responsible safe working with GMO and quarantine material.
Europese aanbesteding commisie lab. material
NAC
Biography
Ing. Tanja Bakx-Schotman graduated as microbiological technician in 1989 at Internationale Agrarische Hogeschool Larenstein . .
She started working at the NIOO in 1989, initially for the Department of Bodembiologie. From April 1989 untill April 1990 together with Prof. Dr. Riks Laanbroek, after that from April 1990 until December 1990 with Dr. Wietse de Boer.
After that she was working as molecular technician for Department of Plant Population Biology (1990-2005) together with Dr. Peter van Dijk and colleagues.
And subsequently for the Department of Terrestrial Ecology . Here work now involves all kind of molecular techniques in several projects.
1994-... Labmanager molecular laboratory
1996-... Biosafety officer: responisble for the license applications and supervision for working with Genetic Modified Organism at the MLI and MLII level.
2004-... Member of the NIOO apparatus Commitee ( NAC)
2009-... Biosafety officer: responsible for the license applications and supervision for working with Genetic Modified Organism at the PCI, PKI, PKII,PCMI, PCMII, PKMIand PKMII level.
2012-... Responsible for the license application from NVWA for working with quarantaine soil.
2016-... Member of the commitee European tender for laboratory necessities ( chemicals, disposables, equipment etc.)
Publications
Peer-reviewed publications
Pioneer Arabidopsis thaliana spans the succession gradient revealing a diverse root-associated microbiome
https://doi.org/10.1186/s40793-023-00511-yBACKGROUND: Soil microbiomes are increasingly acknowledged to affect plant functioning. Research in molecular model species Arabidopsis thaliana has given detailed insights of such plant-microbiome interactions. However, the circumstances under which natural A. thaliana plants have been studied so far might represent only a subset of A. thaliana's full ecological context and potential biotic diversity of its root-associated microbiome.
RESULTS: We collected A. thaliana root-associated soils from a secondary succession gradient covering 40 years of land abandonment. All field sites were situated on the same parent soil material and in the same climatic region. By sequencing the bacterial and fungal communities and soil abiotic analysis we discovered differences in both the biotic and abiotic composition of the root-associated soil of A. thaliana and these differences are in accordance with the successional class of the field sites. As the studied sites all have been under (former) agricultural use, and a climatic cline is absent, we were able to reveal a more complete variety of ecological contexts A. thaliana can appear and sustain in.
CONCLUSIONS: Our findings lead to the conclusion that although A. thaliana is considered a pioneer plant species and previously almost exclusively studied in early succession and disturbed sites, plants can successfully establish in soils which have experienced years of ecological development. Thereby, A. thaliana can be exposed to a much wider variation in soil ecological context than is currently presumed. This knowledge opens up new opportunities to enhance our understanding of causal plant-microbiome interactions as A. thaliana cannot only grow in contrasting soil biotic and abiotic conditions along a latitudinal gradient, but also when those conditions vary along a secondary succession gradient. Future research could give insights in important plant factors to grow in more ecologically complex later-secondary succession soils, which is an impending direction of our current agricultural systems.
Soil microbial diversity and community composition during conversion from conventional to organic agriculture
It is generally assumed that the dependence of conventional agriculture on artificial fertilizers and pesticides strongly impacts the environment, while organic agriculture relying more on microbial functioning may mitigate these impacts. However, it is not well known how microbial diversity and community composition change in conventionally managed farmers' fields that are converted to organic management. Here, we sequenced bacterial and fungal communities of 34 organic fields on sand and marine clay soils in a time series (chronosequence) covering 25 years of conversion. Nearby conventional fields were used as references. We found that community composition of bacteria and fungi differed between organic and conventionally managed fields. In the organic fields, fungal diversity increased with time since conversion. However, this effect disappeared when the conventional paired fields were included. There was a relationship between pH and soil organic matter content and the diversity and community composition of bacteria and fungi. In marine clay soils, when time since organic management increased, fungal communities in organic fields became more dissimilar to those in conventional fields. We conclude that conversion to organic management in these Dutch farmers' fields did not increase microbial community diversity. Instead, we observed that in organic fields in marine clay when time since conversion increased soil fungal community composition became progressively dissimilar from that in conventional fields. Our results also showed that the paired sampling approach of organic and conventional fields was essential in order to control for environmental variation that was otherwise unaccounted for.https://doi.org/10.1111/mec.16571Competition and predation as possible causes of bacterial rarity
https://doi.org/10.1111/1462-2920.14569We assembled communities of bacteria and exposed them to different nutrient concentrations with or without predation by protists. Taxa that were rare in the field were less abundant at low nutrient concentrations than common taxa, independent of predation. However, some taxa that were rare in the field became highly abundant in the assembled communities, especially under ample nutrient availability. This high abundance points at a possible competitive advantage of some rare bacterial taxa under nutrient-rich conditions. In contrast, the abundance of most rare bacterial taxa decreased at low resource availability. Since low resource availability will be the prevailing situation in most soils, our data suggests that under those conditions poor competitiveness for limiting resources may contribute to bacterial rarity. Interestingly, taxa that were rare in the field and most successful under predator-free conditions in the lab also tended to be more reduced by predation than common taxa. This suggests that predation contributes to rarity of bacterial taxa in the field. We further discuss whether there may be a trade-off between competitiveness and predation resistance. The substantial variability among taxa in their responses to competition and predation suggests that other factors, for example abiotic conditions and dispersal ability, also influence the local abundance of soil bacteria. This article is protected by copyright. All rights reserved.
Relationships between fungal community composition in decomposing leaf litter and home-field advantage effects
Increasing evidence suggests that specific interactions between microbial decomposers and plant litter, named home field advantage (HFA), influence litter breakdown. However, we still have limited understanding of whether HFA relates to specific microbiota, and whether specialized microbes originate from the soil or from the leaf microbiome. Here, we disentangle the roles of soil origin, litter types, and the microbial community already present on the leaf litter in determining fungal community composition on decomposing leaf litter and HFA.https://doi.org/10.1111/1365-2435.13351
We collected litters and associated soil samples from a secondary succession gradient ranging from herbaceous vegetation on recently abandoned ex‐arable fields to forest representing the end stage of succession. In a greenhouse, sterilized and unsterilized leaf litters were decomposed for 12 months in soils from early to late successional stages according to a full factorial design. At the end, we examined fungal community composition on the decomposing litter.
Fungal communities on decomposed late‐successional litter in late‐successional soil differed from those in early‐ and mid‐successional stage litter and soil combinations. Soil source had the strongest impact on litter fungal composition when using sterilized litter, while the impact of litter type was strongest when using unsterilized litter. Overall, we observed HFA, as litter decomposition was accelerated in home soils. Increasing HFA did not relate to the dissimilarity in overall fungal composition, but there was increasing dissimilarity in the relative abundance of the most dominant fungal taxon between decomposing litter in home and away soils.
We conclude that early, mid and late succession litter types did not exert strong selection effects on colonization by microorganisms from the soil species pool. Instead, fungal community composition on decomposing litter differed substantially between litter types for unsterilized litter, suggesting that the leaf microbiome, either directly or indirectly, is an important determinant of fungal community composition on decomposing leaves. HFA related most strongly to the abundance of the most dominant fungal taxa on the decomposing litter, suggesting that HFA may be attributed to some specific dominant fungi rather than to responses of the whole fungal community.Plant competition alters the temporal dynamics of plant-soil feedbacks
Most studies on plant‐soil feedback (PSF) and plant competition measure the feedback response at one moment only. However, PSFs and competition may both change over time, and how PSF and competition interact over time is unclear.https://doi.org/10.1111/1365-2745.12999
We tested the temporal dynamics of PSF and interspecific competition for the forb Jacobaea vulgaris and the grass Holcus lanatus. We grew both species individually and in interspecific competition in soil that was first conditioned in the greenhouse by J. vulgaris, by H. lanatus or without plant growth. For a period of 11 weeks, we harvested plants twice a week and analysed the fungal and chemical composition of the different soils at the end of the first and second growth phase.
During the second growth phase, when grown in isolation, both species produced more biomass in heterospecific conditioned soil than in conspecific conditioned soil. Young J. vulgaris exhibited a strong negative conspecific feedback, but this effect diminished over time and became neutral in older plants. In contrast, when grown in competition, the negative conspecific feedback of J. vulgaris exacerbated over time. Older H. lanatus plants benefited more from heterospecific conditioning when competing with J. vulgaris, then when grown isolated.
Fungal community composition and soil chemistry differed significantly between soils but this was mainly driven by differences between plant‐conditioned and unconditioned soils. Remarkably, at the end of the second growth phase, fungal community composition was not explained by the legacy of the species that had been grown in the soil most recently, but still reflected the legacy of the first growth phase. We reexamined plant growth during a third growth phase. Biomass of J. vulgaris was still influenced by the treatments imposed during the first phase, while H. lanatus responded only to the plant growth treatments imposed during the second phase.
Synthesis. Our study shows that the direction and magnitude of PSF depends on plant age and competition, and also on soil legacy effects of earlier plant growth. These results highlight the need to incorporate dynamic PSFs in research on plant populations and communities.Plants Know Where It Hurts: Root and Shoot Jasmonic Acid Induction Elicit Differential Responses in Brassica oleracea
Plants respond to herbivore attack by rapidly inducing defenses that are mainly regulated by jasmonic acid (JA). Due to the systemic nature of induced defenses, attack by root herbivores can also result in a shoot response and vice versa, causing interactions between above- and belowground herbivores. However, little is known about the molecular mechanisms underlying these interactions. We investigated whether plants respond differently when roots or shoots are induced. We mimicked herbivore attack by applying JA to the roots or shoots of Brassica oleracea and analyzed molecular and chemical responses in both organs. In shoots, an immediate and massive change in primary and secondary metabolism was observed. In roots, the JA-induced response was less extensive and qualitatively different from that in the shoots. Strikingly, in both roots and shoots we also observed differential responses in primary metabolism, development as well as defense specific traits depending on whether the JA induction had been below- or aboveground. We conclude that the JA response is not only tissue-specific but also dependent on the organ that was induced. Already very early in the JA signaling pathway the differential response was observed. This indicates that both organs have a different JA signaling cascade, and that the signal eliciting systemic responses contains information about the site of induction, thus providing plants with a mechanism to tailor their responses specifically to the organ that is damaged.https://doi.org/10.1371/journal.pone.0065502Matgrass sward plant species benefit from soil organisms
Soilorganisms are important in the structuring of plant communities. However, little is known about how to apply this knowledge to vegetation management. Here, we examined if soilorganisms may promote plantspecies of characteristic habitats, and suppress plantspecies of disturbed habitats. We classified nineteen fields into four types: characteristic and disturbed matgrass swards and successfully and unsuccessfully restored fields. We recorded the vegetation composition and measured biotic and abiotic soil characteristics of the sites. In a pot experiment, we mixed non-sterilized (with soilorganisms) or sterilized (without soilorganisms) soil inoculum from each field with a common sterilized background soil. We planted seedlings of characteristic matgrass speciesAntennaria dioica and Nardus stricta, of disturbance indicators Deschampsia flexuosa and Agrostis capillaris, or a combination of the four species. At harvest, we measured root and shoot dry mass of all plants. The vegetation composition of characteristic matgrass swards differed from the disturbed and unsuccessfully restored fields. The successfully restored fields were intermediate. The composition of the nematode community tended to follow the same pattern. In the pot experiment, addition of soilorganisms increased the biomass of A. dioica, N. stricta and D. flexuosa, but decreased the biomass of A. capillaris. However, the effect of soilorganisms on plant biomass was not related to field type. A. dioica showed a large variation in biomass in non-sterilized, but not in sterilized soil. Soilorganisms from some sites increased plant biomass, whereas soilorganisms from other sites did not. The biomass of characteristic matgrass plants was lower in the presence of plants from disturbed swards, irrespective of the presence of soilorganisms. Probably A. capillaris was so much larger than the other species, that this overruled effects of added soilorganisms. Soilorganisms promoted growth of plantspecies characteristic of matgrass swards, whereas they reduced growth of a plantspecies characteristic of disturbed fields. Soilorganisms did not change the outcome of plant interactions, which was won by a disturbance indicator. Nevertheless, measurement of the growth stimulating capacity of a soil may be used to assess opportunities for reintroduction of characteristic plantspecies.https://doi.org/10.1016/j.apsoil.2012.07.012Genetic fine-mapping of DIPLOSPOROUS in Taraxacum (dandelion; Asteraceae) indicates a duplicated DIP-gene
Background DIPLOSPOROUS (DIP) is the locus for diplospory in Taraxacum, associated to unreduced female gamete formation in apomicts. Apomicts reproduce clonally through seeds, including apomeiosis, parthenogenesis, and autonomous or pseudogamous endosperm formation. In Taraxacum, diplospory results in first division restitution (FDR) nuclei, and inherits as a dominant, monogenic trait, independent from the other apomixis elements. A preliminary genetic linkage map indicated that the DIP-locus lacks suppression of recombination, which is unique among all other map-based cloning efforts of apomeiosis to date. FDR as well as apomixis as a whole are of interest in plant breeding, allowing for polyploidization and fixation of hybrid vigor, respectively. No dominant FDR or apomixis genes have yet been isolated. Here, we zoom-in to the DIP-locus by largely extending our initial mapping population, and by analyzing (local) suppression of recombination and allele sequence divergence (ASD). Results We identified 24 recombinants between two most closely linked molecular markers to DIP in an F1-population of 2227 plants that segregates for diplospory and lacks parthenogenesis. Both markers segregated c. 1:1 in the entire population, indicating a 1:1 segregation rate of diplospory. Fine-mapping showed three amplified fragment length polymorphisms (AFLPs) closest to DIP at 0.2 cM at one flank and a single AFLP at 0.4 cM at the other flank. Our data lacked strong evidence for ASD at marker regions close to DIP. An unexpected bias towards diplosporous plants among the recombinants (20 out of 24) was found. One third of these diplosporous recombinants showed incomplete penetrance of 50-85% diplospory. Conclusions Our data give interesting new insights into the structure of the diplospory locus in Taraxacum. We postulate a locus with a minimum of two DIP-genes and possibly including one or two enhancers or cis-regulatory elements on the basis of the bias towards diplosporous recombinants and incomplete penetrance of diplospory in some of them. We define the DIP-locus to 0.6 cM, which is estimated to cover ~200-300 Kb, with the closest marker at 0.2 cM. Our results confirm the minor role of suppression of recombination and ASD around DIP, making it an excellent candidate to isolate via a chromosome-walking approach.https://doi.org/10.1186/1471-2229-10-154Plant defence against nematodes is not mediated by changes in the soil microbial community
1. Indirect plant defence, the recruitment of antagonists of herbivores, is well-known above the ground. In spite of various soil microorganisms acting as antagonists to root herbivores, it is still largely unknown whether plants can promote antagonistic microorganisms as an indirect defence mechanism. 2. In a greenhouse study we examined whether soil microorganisms could mediate plant defence against plant-feeding nematodes. Growth, nutrient contents and root exudation of three plant species (Plantago lanceolata, Holcus lanatus, Lotus corniculatus) and the performance of nematodes and fungal communities in the rhizospheres were measured. 3. The plant species differed in their effects on plant-feeding nematodes; however, the addition of soil microorganisms did not enhance nematode control. Nematode addition changed root exudation patterns and rhizosphere fungal community structure in a plant species-specific manner. Glucose levels in the root exudates of all three examined plant species were enhanced, and P. lanceolata root exudates contained higher levels of fumaric acid when nematodes had been added. 4. We conclude that nematodes have plant species-specific effects on root exudate chemistry and rhizosphere fungal community composition, but these effects do not necessarily enhance indirect control of nematodes by antagonistic microorganisms. More studies on below-ground plant defence are definitely needed.https://doi.org/10.1111/j.1365-2435.2009.01543.xMicrobe-mediated plant-soil feedback causes historical contingency effects in plant community assembly
Plant–soil feedback affects performance and competitive ability of individual plants. However, the importance of plant–soil feedback in historical contingency processes and plant community dynamics is largely unknown. In microcosms, we tested how six early-successional plant species of secondary succession on ex-arable land induced plant-specific changes in soil community composition. Following one growth cycle of conditioning the soil community, soil feedback effects were assessed as plant performance in soil of their own as compared to soil from a mixture of the other five early-successional species. Performance was tested in monocultures and in mixed communities with heterospecific competition from mid-successional species. The role of soil microorganisms was determined by isolating the microbial component from the soil community, re-inoculating microorganisms into sterilized substrate, and analyzing plant biomass responses of the early- and mid-successional species. Plant–soil feedback responses of the early-successional species were negative and significantly increased when the plants were grown in a competitive environment with heterospecifics. In monocultures, three early-successional species experienced negative feedback in soil with a history of conspecifics, while all early-successional species experienced negative feedback when grown with interspecific competition. Interestingly, the nonnative forb Conyza canadensis showed the weakest soil feedback e We conclude that feedback between early-successional plant species and soil microorganisms can play a crucial role in breaking dominance of early-successional plant communities. Moreover the influences on soil microorganism community composition influenced plant community dynamics in the mid-successional plant communities. These results shed new light on how feedback effects between plants and soil organisms in one successional stage result in a biotic legacy effect, which influences plant commuhttps://doi.org/10.1890/06-0502Formation of unreduced megaspores (Diplospory) in apomictic Dandelions (Taraxacum officinale, s.l.) is controlled by a sex-specific dominant locus
In apomictic dandelions, Taraxacum officinale, unreduced megaspores are formed via a modified meiotic division (diplospory). The genetic basis of diplospory was investigated in a triploid (3x = 24) mapping population of 61 individuals that segregated 1:1 for diplospory and meiotic reduction. This population was created by crossing a sexual diploid (2x = 16) with a tetraploid diplosporous pollen donor (4x = 32) that was derived from a triploid apomict. Six different inheritance models for diplospory were tested. The segregation ratio and the tight association with specific alleles at the microsatellite loci MSTA53 and MSTA78 strongly suggest that diplospory is controlled by a dominant allele D on a locus, which we have named DIPLOSPOROUS (DIP). Diplosporous plants have a simplex genotype, Ddd or Dddd. MSTA53 and MSTA78 were weakly linked to the 18S-25S rDNA locus. The D-linked allele of MSTA78 was absent in a hypotriploid (2n = 3x - 1) that also lacked one of the satellite chromosomes. Together these results suggest that DIP is located on the satellite chromosome. DIP is female specific, as unreduced gametes are not formed during male meiosis. Furthermore, DIP does not affect parthenogenesis, implying that several independently segregating genes control apomixis in dandelions.https://doi.org/10.1534/genetics.166.1.483Crosses between sexual and apomictic dandelions (Taraxacum). II. The breakdown of apomixis
Some dandelions are diplosporous gametophytic apomicts. In order to study the inheritance and breakdown of apomixis, crosses were made between diploid sexuals and triploid apomicts. To investigate their breeding system, four nonapomictic diploid and 10 nonapomictic triploid hybrids were pollinated with diploids and the progenies were analysed. Seed fertility was significantly reduced in two diploid hybrids. Nine triploid hybrids were fertile and could be classified into three types, with respect to the composition of their progenies. Type A produced n + n hybrids. Type B produced either a mixture of n + n and 2n + n hybrids, or a mixture of pseudogamous 2n + 0 apomicts and 2n + n hybrids. Type C produced exclusively 2n + n hybrids. Inheritance of a microsatellite marker strongly suggested that 2n egg cells in type C plants were produced by a first division restitution mechanism. As in apomicts, microsporogenesis in type C plants was reductional. This suggests that type C plants are diplosporous plants that lack parthenogenesis. Such plants are very rare in other apomictic plant species. It is concluded that 'elements of apomixis', diplospory and parthenogenesis, can be uncoupled. This is inconsistent with the single-locus model for apomixis in Taraxacum as suggested by Mogie (1992). Instead, our results suggest that several loci are involved in the genetic control of apomixis in Taraxacum. [KEYWORDS: 2n-gametes; apomixis; diplospory; parthenogenesis; pseudogamy;Taraxacum Fertilization]https://doi.org/10.1038/sj.hdy.6886200Development and characterization of microsatellite markers in the sexual-apomictic complex Taraxacum officinale (dandelion)
Microsatellite markers were developed in Taraxacum officinale to study gene flow between sexual and apomictic plants and to identify clones. Twenty five thousand genomic DNA clones were hybridized with a (CT)(12)D probe. The density of (GA/CT)(n) repeats was estimated at one every 61 kb in the T. officinale genome, which translates to 13 500 repeats per haploid genome. Ninety two percent of 110 positive clones sequenced contained at least one (GA/CT)(n greater than or equal to 5) repeat. Sixteen (CA/GT)(n greater than or equal to 5) and 11 (AT)(n greater than or equal to 5) arrays were also found in these sequences, suggesting some clustering of dinucleotide repeats. Among 50 PCR primer pairs tested, 32 produced bands and 28 of them were polymorphic. Of these polymorphic markers, 15 were putatively single-locus and the other 13 produced only polymorphic fingerprints. Six loci were further characterized for polymorphism and showed between 6 and 32 alleles per locus. Among eight primer pairs used to analyze the progeny of a sexual cross, seven were co-dominant single-locus Mendelian markers, but one (MSTA10) gave a dominant pattern in accordance with the hypothesis of a null allele segregating in a Mendelian fashion. Three pairs of loci among 28 showed significant linkages of 10, 21, and 39 cM. Observed and expected heterozygosities in two sexual populations indicate that null alleles may be present at two loci, including MSTA10. [KEYWORDS: microsatellites; null alleles; apomixis; silver staining; Taraxacum Simple-sequence repeats; tandem dna repeats; section ruderalia; gene flow; population; abundance; pcr; amplification;deficiency; genomes]https://doi.org/10.1007/s001220050897Chloroplast DNA phylogeography and cytotype geography in autopolyploid Plantago media
In order to gain insight into the causes of parapatric diploid and tetraploid distributions in Plantago media chloroplast DNA (cpDNA) restriction site polymorphism was studied in 36 European populations. Parapatric distributions are often explained by adaptive differences between cytotypes to an underlying heterogeneity in environmental factors. Alternatively, such distribution patterns may be explained nonadaptively, through frequency-dependant production of hybrids with low fitness. However, nonadaptive explanations have been neglected in polyploid Literature. In this study nine chloroplast haplotypes were found. Their phylogeny suggests that tetraploids arose at least three times from diploids. In general, related haplotypes were also geographically clustered, although there were some marked geographical discontinuities. In the Pyrenees, diploids and tetraploids carried diverged haplotypes throughout their parapatric ranges. At the contact zone the level of cpDNA introgression in a mixed diploid- tetraploid population was low. It is discussed that the cpDNA phylogeography supports the nonadaptive hypothesis that parapatric cytotype distributions may be explained by postPleistocene range expansions followed by mutual minority cytotype exclusion, due to hybrid unfitness. [KEYWORDS: phylogeography; cpDNA; polyploidy; hybrid inviability; colonization; Pleistocene Gene flow; saxifragaceae; oaks]https://doi.org/10.1046/j.1365-294X.1997.00199.xThe dynamics of gynodioecy in Plantago lanceolata L. .1. Frequencies of male-steriles and their cytoplasmic male sterility types
The maintenance of a gynodioecious breeding system (hermaphrodites and male-steriles) was studied in Plantago lanceolata. Cytoplasmic-nuclear inheritance is important in the maintenance of male-steriles. The male-sterile trait is cytoplasmically based (CMS), and male fertility can be restored by nuclear genes. Male-sterile frequencies differ among populations. Several hypotheses can be considered. (1) In each population a different equilibrium could be optimal because of environmentally dependent fitnesses. (2) None of the populations has reached an equilibrium (yet). (3) The populations are in different phases of a dynamic equilibrium, i.e. limit cycles. The last two explanations both predict a dynamic process, a continuous change within populations. Sex phenotype frequencies and their underlying gene frequencies were assessed. Sex phenotype frequencies changed over years within populations. We showed that these changes resulted from changes in genotype composition, which favours the two hypotheses (2 and 3) that predict a dynamic process. CMS-type frequencies were estimated using mtDNA markers. Among populations, CMS types differed in frequencies. CMSI and CMSIII seemed to exclude each other, and CMSII types occurred in all populations. In all populations, CMSI appeared to be less restored than the other CMS types. This was not expected on the basis of either of the two theoretical models that included dynamics (hypotheses 2 and 3). [KEYWORDS: cytoplasmic male sterility; dynamic equilibrium; gynodioecy male sterility; Plantago Thymus-vulgaris l; mitochondrial-dna; populations; evolution; coronopus; dioecy]https://doi.org/10.1038/hdy.1997.184