Droevendaalsesteeg 10
6708 PB Wageningen
The Netherlands
Freddy ten Hooven
About
Freddy ten Hooven has expertise with both Molecular and Microbial laboratory techniques. He also manages research facilities such as the Mesocosm and Soil Ecotron and is experienced with sampling expeditions in the field and extractions of soil animals.
Biography
Ing. Freddy ten Hooven graduated from the Hogeschool van Hall Larenstein in 2009, where he studied plant biotechnology. Before that he studied Microbiology and Botany at Mondriaan Onderwijsgroep in Delft where he graduated in 2005.
Freddy did his first internship at the NIOO in Heteren in 2004-2005 where he worked on Glucosinolates in Brassica species with Prof. Dr. Nicole van Dam. His work mainly consisted of greenhouse experiments and HPLC analysis. In 2009 Freddy returned to the NIOO to do another internship on the bacterial- and fungal community composition using TRFLP with Dr. Tess van de Voorde. After graduation in 2009 Freddy worked as a technician at the NIOO for several months.
From 2010 - 2011 Freddy worked for a year at Groen Agro Control as a molecular technician. He was responsible for plant pathogen determination with various techniques like PCR, qPCR, ELISA and morphological determination.
In 2011 Freddy came back to the NIOO where he got a permanent position as technician in 2012. Freddy works mainly at the molecular- and microbial laboratory but is also well known with performing field-, mesocosm-, and greenhouse experiments and the collection and measurements of samples from soil, plants or other sources.
Freddy works together with several scientists from the TE department. For the last few years Freddy was involved in the ERC advanced grant project SPECIALS; of Prof. Dr. Ir. Wim van der Putten and the VENI project Specialists at work of Dr. Ciska Veen. Sincs 2021 he works on the Onder Het Maaiveld (OHM, underneath the mowing field) managing a large Soil Ecotron with different soil types and a national soil sampling program together with others from the OHM team.
Dossier
Invasive speciesResearch Expertise
Above-belowground interactions Bacteria Bio-informatics DNA-isolation Field experiments Fungi determination Fungi-oomycete isolation Greenhouse experiments Laboratory management Metagenomics Microbiology Molecular biology Nematodes Next-generation sequencing PCR Python qPCR R Terrestrial ecologyCV
Publications
Peer-reviewed publications
Contrasting effects of soil microbial interactions on growth–defence relationships between early- and mid-successional plant communities
https://doi.org/10.1111/nph.17609Plants allocate resources to processes related to growth and enemy defence. Simultaneously, they interact with complex soil microbiomes that also affect plant performance. While the influence of individual microbial groups on single plants is increasingly studied, effects of microbial interactions on growth, defence and growth–defence relationships remain unknown, especially at the plant community level. We investigated how three microbial groups (bacteria, fungi, protists), alone and in full-factorial combinations, affect plant performance and potential growth–defence relationships by measuring phenolics composition in early- and mid-successional grass and forb communities in a glasshouse experiment. Microbial groups did not affect plant growth and only fungi increased defence compounds in early- and mid-successional forbs, while grasses were not affected. Shoot biomass–defence relationships were negatively correlated in most microbial treatments in early-successional forbs, but positively in several microbial treatments in mid-successional forbs. The growth–defence relationship was generally negative in early-successional but not in mid-successional grasses. The presence of different microbiomes commonly removed the observed growth–defence relationships. We conclude that soil microorganisms and their interactions can shift growth–defence relationships differentially for plant functional groups and the relationships vary between successional stages. Microbial interaction-induced growth–defence shifts might therefore underlie distinct plant strategies and fitness.
Steering the soil microbiome by repeated litter addition
1. Microbial communities drive plant litter breakdown. Litters originating from different plant species are often associated with specialised microbiomes that accelerate the breakdown of that litter, known as home-field advantage. Yet, how and how fast microbial communities specialise towards litter inputs is not known.https://doi.org/10.1111/1365-2745.13662
2. Here we study effects of repeated litter additions on soil microbial community structure and functioning. We set up a 9-month, full-factorial, reciprocal litter transplant experiment with soils and litters from six plant species (three grasses and three trees). We measured fungal and bacterial community composition, litter mass loss and home-field effects.
3. We found that repeated litter additions resulted in convergence in fungal community composition driven by litter functional group (trees vs. grasses). Grasses enriched Sordariomycetes, while Tremellomycetes, Eurotiomycetes and Leotiomycetes were favoured by tree litter. Bacterial community composition, litter mass loss and home-field effects were not affected by litter incubation, but there was a relationship between fungal community composition and mass loss.
4. We conclude that repeated litter incubations can result in directional shifts in fungal community composition, while 9 months of litter addition did not change bacterial community composition and the functioning and specialisation of microbial communities.
5. Testing further how repeated litter inputs affect microbial functioning is essential for steering decomposer communities for optimal soil carbon and nutrient cycling.Fungal root endophytes influence plants in a species-specific manner that depends on plant's growth stage
https://doi.org/10.1111/1365-2745.13584The mycobiome (fungal microbiome) influences plants—from seed germination to full maturation. While many studies on fungal-plant interaction studies have focused on known mutualistic and pathogenic fungi, the functional role of ubiquitous endophytic fungi remains little explored. We examined how root-inhabiting fungi (endophytes) influence range-expanding plant species. We isolated endophytes from three European intra-continental range-expanders and three congenerics that are native both in the range expander's original (southern Europe) and new (northern Europe) range. To standardize our collection, endophytes were obtained from all six plant species growing under controlled conditions in northern (new range of the range expander) and southern (native range of the range expander) soils. We cultivated, molecularly identified and tested the effects of all isolates on seed germination, and growth of seedlings and older plants. Most of the 34 isolates could not be functionally characterized based on their taxonomic identity and literature information on functions. Endophytes affected plant growth in a plant species–endophyte-specific manner, but overall differed between range-expanders and natives. While endophytes reduced germination and growth of range-expanders compared to natives, they reduced seedling growth of natives more than of range-expanders. Synthesis. We conclude that endophytic fungi have a direct effect on plant growth in a plant growth stage-dependent manner. While these effects differed between range expanders and natives, the effect strength and significance varied among the plant genera included in the present study. Nevertheless, endophytes likely influence the establishment of newly arriving plants and influence vegetation dynamics.
‘Home’ and ‘away’ litter decomposition depends on the size fractions of the soil biotic community
The ‘home-field advantage’ (HFA) hypothesis predicts that litter decomposition is accelerated in its home environment (i.e. in conspecific soil). Soil organisms play a key role in driving such HFA effects. Soil biota have a large range of body sizes, referred to as size fractions, which may influence their roles in the decomposition process and in the generation of HFA effects. However, how HFA effects depend on the different size fractions of the soil biotic community is unknown. We conducted a microcosm decomposition experiment to examine how size fractions of the soil biotic community affected litter decomposition and HFA effects. In a semi-natural grassland in the Netherlands, we collected leaf litter and soil from two abundant forbs: Tanacetum vulgare and Jacobaea vulgaris. Watery extracts of the soils were sieved through differently-meshed sieves (ranging from 850 μm to 6 μm) to obtain soil communities of different size fractions. Microcosms were inoculated with these different size fractions of the soil biotic community and we examined their effects on microbial composition, litter mass loss and HFA effects. Three months after inoculation, the diversity of the fungal community in the inoculated pots decreased with decreasing size fractions of the soil biotic community. Similarly, litter mass loss also decreased with decreasing soil biotic community size. In contrast, the HFA effect increased with decreasing size fractions of the soil biotic community, but these differences disappeared after six months of decomposition. Our results indicate that soil microorganisms, mainly the smallest size fractions, are specialized to decompose specific resources and thus promote HFA effects, but that their effect is only apparent during specific stages of litter decomposition.https://doi.org/10.1016/j.soilbio.2020.107783Latitudinal variation in soil nematode communities under climate warming-related range-expanding and native plants
Current climate change has led to latitudinal and altitudinal range expansions of numerous species. During such range expansions, plant species are expected to experience changes in interactions with other organisms, especially with belowground biota that have a limited dispersal capacity. Nematodes form a key component of the belowground food web as they include bacterivores, fungivores, omnivores and root herbivores. However, their community composition under climate change‐driven intracontinental range‐expanding plants has been studied almost exclusively under controlled conditions, whereas little is known about actual patterns in the field. Here, we use novel molecular sequencing techniques combined with morphological quantification in order to examine nematode communities in the rhizospheres of four range‐expanding and four congeneric native species along a 2,000 km latitudinal transect from South‐Eastern to North‐Western Europe. We tested the hypotheses that latitudinal shifts in nematode community composition are stronger in range‐expanding plant species than in congeneric natives and that in their new range, range‐expanding plant species accumulate fewest root‐feeding nematodes. Our results show latitudinal variation in nematode community composition of both range expanders and native plant species, while operational taxonomic unit richness remained the same across ranges. Therefore, range‐expanding plant species face different nematode communities at higher latitudes, but this is also the case for widespread native plant species. Only one of the four range‐expanding plant species showed a stronger shift in nematode community composition than its congeneric native and accumulated fewer root‐feeding nematodes in its new range. We conclude that variation in nematode community composition with increasing latitude occurs for both range‐expanding and native plant species and that some range‐expanding plant species may become released from root‐feeding nematodes in the new range.https://doi.org/10.1111/gcb.14657Range-expansion effects on the belowground plant microbiome
Plant range expansion is occurring at a rapid pace, largely in response to human-induced climate warming. Although the movement of plants along latitudinal and altitudinal gradients is well-documented, effects on belowground microbial communities remain largely unknown. Furthermore, for range expansion, not all plant species are equal: in a new range, the relatedness between range-expanding plant species and native flora can influence plant–microorganism interactions. Here we use a latitudinal gradient spanning 3,000 km across Europe to examine bacterial and fungal communities in the rhizosphere and surrounding soils of range-expanding plant species. We selected range-expanding plants with and without congeneric native species in the new range and, as a control, the congeneric native species, totalling 382 plant individuals collected across Europe. In general, the status of a plant as a range-expanding plant was a weak predictor of the composition of bacterial and fungal communities. However, microbial communities of range-expanding plant species became more similar to each other further from their original range. Range-expanding plants that were unrelated to the native community also experienced a decrease in the ratio of plant pathogens to symbionts, giving weak support to the enemy release hypothesis. Even at a continental scale, the effects of plant range expansion on the belowground microbiome are detectable, although changes to specific taxa remain difficult to decipher.https://doi.org/10.1038/s41559-019-0828-zSoil functional responses to drought under range-expanding and native plant communities
Current climate warming enables plant species and soil organisms to expand their range to higher latitudes and altitudes. At the same time, climate change increases the incidence of extreme weather events such as drought. While it is expected that plants and soil organisms originating from the south are better able to cope with drought, little is known about the consequences of their range shifts on soil functioning under drought events.https://doi.org/10.1111/1365-2435.13453
Here, we test how range‐expanding plant species and soil communities may influence soil functioning under drought. We performed a full‐factorial outdoor mesocosm experiment with plant communities of range expanders or related natives, with soil inocula from the novel or the original range, with or without summer drought. We measured litter decomposition, carbon mineralization and enzyme activities, substrate‐induced respiration, and the relative abundance of soil saprophytic fungi immediately after drought and at 6 and 12 weeks after rewetting.
Drought decreased all soil functions regardless of plant and soil origin except one; soil respiration was less reduced in soils of range‐expanding plant communities, suggesting stronger resistance to drought. After rewetting, soil functioning responses depended on plant and soil origin. Soils of native plant communities with a history of drought had more litter mass loss and higher relative abundance of saprophytic fungi than soils without drought and soils of range expanders. Functions of soil from range expanders recovered in a more conservative manner than soils of natives, as litter mass loss did not exceed the control rates. At the end of the experiment, after rewetting, most soil functions in mesocosms with drought history did not differ anymore from the control.
We conclude that functional consequences of range expanding plants and soil biota may interact with effects of drought, and that these effects are most prominent during the first weeks after rewetting of the soil.Integrating quantitative morphological and qualitative molecular methods to analyse soil nematode community responses to plant range expansion
Below‐ground nematodes are important for soil functioning, as they are ubiquitous and operate at various trophic levels in the soil food web. However, morphological nematode community analysis is time consuming and requires ample training. qPCR‐based nematode identification techniques are well available, but high‐throughput sequencing (HTS) might be more suitable for non‐targeted nematode community analyses.https://doi.org/10.1111/2041-210X.12999
We compared effectiveness of qPCR‐ and HTS‐based approaches with morphological nematode identification while examining how climate warming‐induced plant range expansion may influence below‐ground nematode assemblages. We extracted nematodes from soil of Centaurea stoebe and C. jacea populations in Slovenia, where both plant species are native, and Germany, where C. stoebe is a range expander and C. jacea is native. Half of each nematode sample was identified morphologically and the other half was analysed using targeted qPCR and a novel HTS approach.
HTS produced the highest taxonomic resolution of the nematode community. Nematode taxa abundances correlated between the methods. Therefore, especially relative HTS and relative morphological data revealed nearly identical ecological patterns. All methods showed lower numbers of plant‐feeding nematodes in rhizosphere soils of C. stoebe compared to C. jacea. However, a profound difference was observed between absolute and relative abundance data; both sampling origin and plant species affected relative abundances of bacterivorous nematodes, whereas there was no effect on absolute abundances.
Taken together, as HTS correlates with relative analyses of soil nematode communities, while providing highest taxonomic resolution and sample throughput, we propose a combination of HTS with microscopic counting to supplement important quantitative data on soil nematode communities. This provides the most cost‐effective, in‐depth methodology to study soil nematode community responses to changes in the environment. This methodology will also be applicable to nematode analyses in aquatic systems.Drought legacy effects on the composition of soil fungal and prokaryote communities
It is increasingly acknowledged that climate change is influencing terrestrial ecosystems by increased drought and rainfall intensities. Soil microbes are key drivers of many processes in terrestrial systems and rely on water in soil pores to fulfill their life cycles and functions. However, little is known on how drought and rainfall fluctuations, which affect the composition and structure of microbial communities, persist once original moisture conditions have been restored. Here, we study how simulated short-term drying and re-wetting events shape the community composition of soil fungi and prokaryotes. In a mesocosm experiment, soil was exposed to an extreme drought, then re-wetted to optimal moisture (50% WHC, water holding capacity) or to saturation level (100% WHC). Composition, community structure and diversity of microbes were measured by sequencing ITS and 16S rRNA gene amplicons 3 weeks after original moisture content had been restored. Drying and extreme re-wetting decreased richness of microbial communities, but not evenness. Abundance changes were observed in only 8% of prokaryote OTUs, and 25% of fungal OTUs, whereas all other OTUs did not differ between drying and re-wetting treatments. Two specific legacy response groups (LRGs) were observed for both prokaryotes and fungi. OTUs belonging to the first LRG decreased in relative abundance in soil with a history of drought, whereas OTUs that increased in soil with a history of drought formed a second LRG. These microbial responses were spread among different phyla. Drought appeared to be more important for the microbial community composition than the following extreme re-wetting. 16S profiles were correlated with both inorganic N concentration and basal respiration and ITS profiles correlated with fungal biomass. We conclude that a drying and/or an extreme re-wetting history can persist in soil microbial communities via specific response groups composed of members with broad phylogenetic origins, with possible functional consequences on soil processes and plant species. As a large fraction of OTUs responding to drying and re-wetting belonged to the rare biosphere, our results suggest that low abundant microbial species are potentially important for ecosystem responses to extreme weather events.https://doi.org/10.3389/fmicb.2018.00294Transient negative biochar effects on plant growth are strongest after microbial species loss
Biochar has been explored as an organic amendment to improve soil quality and benefit plant growth. The overall positive effects of biochar on crop yields are generally attributed to abiotic changes, while the alternative causal pathway via changes in soil biota is unexplored. We compared plant growth effects of legumes in sterile soil inoculated with dilutions of soil and soil microbial suspensions to determine the direct effects of biochar-induced changes in soil biota on plant growth. Suspensions and soil were from soil amended with biochar and soil without biochar. By comparing consecutive plant growth phases on the same inoculated soils, we also determined the temporal effects of soil biota from biochar-amended and control soils. Biota from biochar-amended soil was less beneficial for Medicago sativa growth, especially with small amounts of inocula. Flowering was delayed in the presence of biota from biochar plots. Inoculum with either soil or soil suspension gave similar results for plant biomass, indicating that microorganisms play a major role. Vicia villosa growth did not respond to the various inocula, even though the inoculum quantity strongly affected nematode community composition and protozoan abundance. In a later growing phase the negative effect of biochar-associated biota on Medicago growth mostly disappeared, which leads to the conclusion that the benefits of biochar application via abiotic changes may outweigh the negative effects of biochar on soil biota.https://doi.org/10.1016/j.soilbio.2017.09.016Seed and root endophytic fungi in a range expanding and a related plant species
Climate change is accelerating the spread of plants and their associated species to new ranges. The differences in range shift capacity of the various types of species may disrupt long-term co-evolved relationships especially those belowground, however, this may be less so for seed-borne endophytic microbes. We collected seeds and soil of the range-expanding Centaurea stoebe and the congeneric C. jacea from three populations growing in Slovenia (native range of both Centaurea species) and the Netherlands (expanded range of C. stoebe, native range of C. jacea). We isolated and identified endophytic fungi directly from seeds, as well as from roots of the plants grown in Slovenian, Dutch or sterilized soil to compare fungal endophyte composition. Furthermore, we investigated whether C. stoebe hosts a reduced community composition of endophytes in the expanded range due to release from plant-species specific fungi while endophyte communities in C. jacea in both ranges are similar.We cultivated 46 unique and phylogenetically diverse endophytes. A majority of the seed endophytes resembled potential pathogens, while most root endophytes were not likely to be pathogenic. Only one endophyte was found in both roots and seeds, but was isolated from different plant species. Unexpectedly, seed endophyte diversity of southern C. stoebe populations was lower than of populations from the north, while the seed endophyte community composition of northern C. stoebe populations was significan...https://doi.org/10.3389/fmicb.2017.01645Interspecific differences in nematode control between range-expanding plant species and their congeneric natives
Climate change enables range expansions of plants, animals and microbes to higher altitudes and latitudes. Plants may benefit from range expansion when they escape from natural enemies. However, range expansion becomes a disadvantage when plants become disconnected from organisms that control enemies in the new range. Here, we examined nematode control in the root zone of range-expanding plant species and congeneric natives. In a greenhouse, we determined bottom-up (by the plants) and top-down (by natural enemies of the nematodes) control of two root-feeding nematode species (Helicotylenchus pseudorobustus and Meloidogyne hapla) in the rhizospheres of two range-expanding plant species, Centaurea stoebe and Geranium pyrenaicum, and two congeneric natives, Centaurea jacea and Geranium molle. Pots with plants growing in sterilized soil were inoculated with either a microbial soil community from the newly colonized natural habitat, a mixture of native microbial nematode antagonists, or a combination of these two communities. We tested the hypotheses that bottom-up control of root-feeding nematodes would be strongest in the root zone of range expanders and that top-down control would be strongest in the root zone of native plant species. We observed profound intra- and interspecific differences in bottom-up and top-down control among all four plant species. Bottom-up control by the range-expanding plant species was either strong or weak. Top-down control by microbes was strongest in native Centaurea. The addition of a mixture of both microbial communities reduced control of M. hapla in the root zones of the native plant species, and enhanced its control in the root zones of range-expanding plant species. We conclude that there was species-specific bottom-up and top-down control of root-feeding nematodes among the four plant species tested. Range-expanding plant species influenced their microbial rhizosphere community differently compared to native plant species, but top-down control in the root zone of natives was not systematically superior to that of range-shifting plant species.https://doi.org/10.1016/j.soilbio.2016.06.025Competition increases sensitivity of wheat (Triticum aestivum) to biotic plant-soil feedback
Plant-soil feedback (PSF) and plant competition play an important role in structuring vegetation composition, but their interaction remains unclear. Recent studies suggest that competing plants could dilute pathogenic effects, whereas the standing view is that competition may increase the sensitivity of the focal plant to PSF. In agro-ecosystems each of these two options would yield contrasting outcomes: reduced versus enhanced effects of weeds on crop biomass production. To test the effect of competition on sensitivity to PSF, we grew Triticum aestivum (Common wheat) with and without competition from a weed community composed of Vicia villosa, Chenopodium album and Myosotis arvensis. Plants were grown in sterilized soil, with or without living field inoculum from 4 farms in the UK. In the conditioning phase, field inocula had both positive and negative effects on T. aestivum shoot biomass, depending on farm. In the feedback phase the differences between shoot biomass in T. aestivum monoculture on non-inoculated and inoculated soils had mostly disappeared. However, T. aestivum plants growing in mixtures in the feedback phase were larger on non-inoculated soil than on inoculated soil. Hence, T. aestivum was more sensitive to competition when the field soil biota was present. This was supported by the statistically significant negative correlation between shoot biomass of weeds and T. aestivum, which was absent on sterilized soil. In conclusion, competition in cereal crop-weed systems appears to increase cereal crop sensitivity to soil biota.https://doi.org/10.1371/journal.pone.0066085