Marie Duhamel

Wageningen University & Research | WUR · Wageningen Plant Research

The use of stable-isotope probing (SIP) allows tracing specific labeled substrates into fungi leading to a better understanding of their role in biogeochemical cycles and their relationship with their environment. Stable isotope probing combined with ribosomal RNA molecule, conserved in the three kingdoms of life, and messenger RNA analysis permits...

Many chemical synthetic chemistry plant protection products are going to be forbidden by law. In addition, there is an increasing demand from consumers for residue-free products that have a lesser impact on health and environment. The natural ability of a plant to defend itself against diseases and pests, plant resilience, is an important part of...

Pathogenic Escherichia coli strains are responsible for food-borne disease outbreaks upon consumption of fresh vegetables and fruits. The aim of this study was to establish the transmission route of E. coli strain 0611, as proxy for human pathogenic E. coli, via manure, soil and plant root zones to the above-soil plant compartments. The ecological...

Background and Aim Water is an increasingly scarce resource while some crops, such as paddy rice, require large amounts of water to maintain grain production. A better understanding of rice drought adaptation and tolerance mechanisms could help to reduce this problem. There is evidence of a possible role of root-associated fungi in drought adaptati...

Because interactions between plants and microbial organisms can influence species diversity and rates of nutrient cycling, how plants shape microbial communities is fundamental to understanding the structure of ecosystems. Despite this, the spatial and temporal scales over which plants influence microbial communities is poorly understood, particula...

Symbioses between plants and microbial organisms can fundamentally alter the structure of ecosystems, from their species diversity to rates of nutrient cycling. Yet, many aspects of how differences in the prevalence of microbial symbioses arise are unclear. This is a key knowledge gap, as if co-variation in plant and microbial distributions are pri...

Background Within the root endosphere, fungi are known to be important for plant nutrition and resistance to stresses. However, description and understanding of the rules governing community assembly in the fungal fraction of the plant microbiome remains scarce. Methods We used an innovative DNA- and RNA-based analysis of co-extracted nucleic acid...

Supplementary material: Figs S1, S2, S3, S4 and S5; Table S1 Figure S1. Mean rarefaction curves of 19 samples. Coloured area (i.e., RNA fraction in red, DNA fraction in blue) indicates ±SE. Figure S2. Taxonomic distribution of sequences in the DNA and the RNA fractions. The mean relative sequence abundance and standard error are shown for the domin...

In this study we use a unique system where the past history of vegetation is well known in order to quantify how plant species establishment influences development of microbial communities and microbe mediated ecosystem functions.

The use of stable-isotope probing (SIP) allows tracing specifi c labeled substrates into fungi leading to a better understanding of their role in biogeochemical cycles and their relationship with their environment. Stable-isotope probing combined with ribosomal RNA molecule, conserved in the three kingdoms of life, and messenger RNA analysis permit...

Microbes show more geographic diversity than previously expected, a serious challenge for ecological prediction. However, a recent study shows that microbial communities from a global grassland plot network responded consistently to nutrient addition. These results highlight the risks of nutrient deposition, but also hope for generalized understand...

Plants and soil microbial communities are intimately linked through their respective influence on the abiotic soil environment. Plants may influence soil chemistry through the quality and quantity of litter and rhizosphere inputs, and microbial breakdown and transformation of these organic compounds in turn can influence plant nutrient uptake and f...

Plants can no longer be considered as standalone entities and a more holistic perception is needed. Indeed, plants harbor a wide diversity of microorganisms both inside and outside their tissues, in the endosphere and ectosphere, respectively. These microorganisms, which mostly belong to Bacteria and Fungi, are involved in major functions such as p...

Food demand will increase concomitantly with human population. Food production therefore needs to be high enough and, at the same time, minimize damage to the environment. This equation cannot be solved with current strategies. Based on recent findings, new trajectories for agriculture and plant breeding which take into account the belowground comp...

A key objective in ecology is to understand how cooperative strategies evolve and are maintained in species networks. Here, we focus on the tri-trophic relationship between arbuscular mycorrhizal (AM) fungi, host plants, and fungivores to ask if host plants are able to protect their mutualistic mycorrhizal partners from being grazed. Specifically,...

The mutualism between plants and arbuscular mycorrhizal fungi is extremelywidespread (~ 80% of plants are colonized by these organisms) and ancient (over 450 million years ago). This symbiotic relationship is an essential component of healthy ecosystem functioning and productivity, and is strongly involved in the cycle of two key elements: phosphor...

Background: In environmental sequencing studies, fungi can be identified based on nucleic acid sequences, using either highly variable sequences as species barcodes or conserved sequences containing a high-quality phylogenetic signal. For the latter, identification relies on phylogenetic analyses and the adoption of the phylogenetic species concept...

MySQL table structure of PHYMYCO-DB. (TIF)

Plants and their arbuscular mycorrhizal fungal symbionts interact in complex underground networks involving multiple partners. This increases the potential for exploitation and defection by individuals, raising the question of how partners maintain a fair, two-way transfer of resources. We manipulated cooperation in plants and fungal partners to sh...