Droevendaalsesteeg 10
6708 PB Wageningen
The Netherlands
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
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.)
Soil organisms at higher trophic positions in the food web, such as nematodes or protists, play a key role in shaping the composition and functioning of soil communities. However, intensive agriculture can put these organisms under pressure and restoring communities of soil organisms will be vital for a more sustainable functioning of agricultural soils. Here, we examine how changing land use from conventional to organic farming influences the composition and diversity of belowground nematodes and protists. We collected soil samples from 68 organic and conventional farmers’ fields on clay and sandy soils and used 18S sequencing to determine soil community composition and diversity. In order to test effects of time since conversion from conventional to organic management, we used organically farmed soils that had been converted at time periods varying from 1 to 25 years ago, each being paired with a nearby conventional field in order to account for local environmental differences in climate and soil conditions. The ASV richness and Shannon diversity of protists was lowest in organic fields and while protist community composition differed between organic and conventional fields in clay soils, effects were relatively minor. Similarly, Shannon diversity of nematodes was lower in organic fields at clay soil, but there was no difference in nematode community composition and species richness between conventional and organic fields. Progressing time since conversion to organic management impacted community composition for both nematodes and protists in clay soils and led to an increased protist richness and diversity in both clay and sandy soils. However, we found a similar trend for the conventional fields if we assigned them the age of the paired organic field, suggesting that the observed shifts may not have been driven by time since conversion alone, but also by other hitherto unidentified factors. Although pH, soil organic matter content, and microbial biomass were not related to time since conversion, they could explain functional and taxonomic community composition of both nematodes and protists. Shifts in the relative abundance of feeding/functional groups of protists and nematodes were variable and depended on soil and management type. We conclude that conversion from conventional to organic management influenced protist and nematode diversity and community composition, but effects were relatively minor and dependent on sand versus clay soil. Further studies are needed to determine functional implications of the shifts in protist and nematode community composition for functioning of the organic versus conventionally farmed soils.
BACKGROUND: 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.
We 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.