Interactions between rice, Meloidogyne graminicola & microbiota (2018-2021)

At the end of my master, I did an internship under the supervision of Stéphane Bellafiore and Lionel Moulin in the unit research PHIM (Plant Health Institute of Montpellier). We were focusing on a plant pathosystem (rice & Meloidogyne graminicola) that I already knew (from my DUT internship and gap year) but complexifying the study of their interactions by integrating root-associated bacteria in the system. Our working hypothesis on this tripartite model (rice, nematode & bacteria) was that the presence of root-associated bacteria could directly or indirectly impact the nematode infection by different mechanisms of interaction. After having found evidences that the three entities were indeed interacting, we proposed a thesis subject at the doctoral school GAIA and I obtained a grant for three years. I am glad this subject challenged me on technical and intellectual aspects, trying to integrate more environmental components (soil microorganisms) to have a bigger picture on the plant pathosystem in the field. You can read the thesis and a brief content here.

Thesis report – MASSON

Title

The root-associated microbiota of rice in different contexts of infection by phytoparasitic nematodes: an ecological approach to a plant pathosystem

Abstract

Plants are interacting with plenty of surrounding organisms in their environment. The effects that emerge can result in detriment or benefit for plants. Nematodes, the most abundant soil animals, are playing a great role in soil fertility and are excellent bioindicators of the soil functioning through their diverse lifestyles. Among them, Meloidogyne graminicola is an obligate parasitic nematode of rice, its main host and a staple food for the human population. During its life cycle in rice, M. graminicola creates a specialized niche at the infection site in roots, called gall, that turns into a nutrient sink for the nematode feeding. It can disrupt the plant growth and ultimately cause a serious grain yield loss. Rapid socio-economic and environmental changes increased this parasitic pressure in rice cropping systems, urging farmers and researchers to consider the disease emergence with an ecological view. Pathogens could indeed cause little damage to plants thanks to a cohort of phytobeneficial microorganisms in disease suppressive soils. Therefore, agricultural systems promoting microbiodiversity such as soil conservation agriculture are brought forward. However, little is known about the complexity of simultaneous effects of biotic and abiotic factors on the plant-parasitic infection in rice cropping systems. In this thesis, we characterized the rice-associated gall microbiome of M. graminicola for the first time, in highly infested fields in Vietnam. Using an amplicon barcoding method on the 16S rRNA coding gene, we observed deep modifications between galls and non-infected roots: a shift in the microbiota structure, a higher richness and diversity, taxa enrichments and a specific network of bacteria able to live in the “gallobiome” (i.e. biome of gall), potentially as opportunistic organisms. In a second step, since we noticed that rice was less infected by M. graminicola seven year after the transition from conventional tillage to conservation agriculture in an experimental field in Cambodia, we could explore the rhizosphere communities of bacteria (16S rRNA), fungi (ITS2 rRNA) and nematodes (microscopic observations) in this cropping system. Under conservation agriculture, we found that there was an accumulation of soil organic matter and nutrients available for plants and basal microorganisms which were more abundant and diversified, especially fungi. Through cascading effects, the soil food web became more mature and potentially harbored more mutualistic organisms for rice and antagonistic organisms to plant-parasitic nematodes. This hypothesis was tested in the last part, using a complementary cultivable method to recover bacterial endophytes from rice roots of the experimental field. We performed in planta tests to measure the potential of single bacterial inoculation to induce indirect beneficial effects on rice infected by M. graminicola, and in vitro tests to measure plant-growth promotion effects and direct effects against M. graminicola. We found phytobeneficial strains exhibiting plant-growth promotion traits, and maintaining the shoot mass while infected, therefore improving the plant tolerance to the nematode infection. Some strains were able to reduce the root galling and/or to antagonize the nematode, and some others were associated with the infection in the field and with the gallobiome, suggesting they could be opportunistic and/or assist the nematode. More research is required to assess the potential of a microbial consortium to cooperatively modulate the interactions in the pathosystem Meloidogyne graminicola – Oryza sativa. The approach used in this thesis revealed that promoting microbiodiversity through agricultural practices is a promising strategy to suppress the disease caused by M. graminicola and sustain rice health.

Keywords

Oryza sativa, amplicon barcoding, gall microbiome, Meloidogyne graminicola, conservation agriculture, soil disease suppressiveness