M2 Project porposal BCE

Host laboratory: Research platform Biochem-Env, UMR1402 ECOSYS, INRAE - Campus Agro Paris-Saclay, Bâtiment F, 22 place de l'Agronomie, CS80022, 91120 Palaiseau cedex

http://www.biochemenv.fr

Internship length: 6 months, starting date flexible

Context and background

Measuring enzymatic activities in environmental samples such as soil, sediments, plants and invertebrates has emerged as one of the key approaches for evaluating ecosystem condition. Therefore, enzymatic activities are widely recognized as important biological indicators of the ecosystem’s health. In terms of soil related research, their advantage comparing to physico-chemical indicators is that they provide an insight into the biochemical dynamics of the soil, provide information regarding soil fertility, and allow us also to follow the processes such as bioremediation, or effects of soil perturbation^1,2.

Polysaccharides such as cellulose, chitin and xylans are highly abundant and widely distributed carbon sources within ecosystems. Their degradation represents one of the crucial steps in the carbon cycle. This process begins with the initial degradation stage, in which endoglycanases enzymatically break down these polysaccharide chains into oligosaccharides^3–5. Following this initial degradation step, released oligosaccharides undergo further digestion by various exolytic enzymes called glycosidases and their associated enzymes, enabling the release of free monosaccharides which can then enter the main carbon metabolic pathways of soil microorganisms. Measuring endoglycanase activity helps reveal the rate at which stored carbon pools are being transformed. Higher activity suggests faster decomposition, while changes in activity may provide important information regarding shifts in soil carbon cycle¹.

The present proposal aims to develop a portable in-gel, high-throughput tool for rapidly measuring glycanase activity in soil samples. The proposed approach is designed to be highly specific, user-friendly, cost-effective, reproducible, and capable of delivering semi-quantitative measurements, enabling scalable assessment of microbial activity across diverse environmental samples. To the best of our knowledge, there is no analogue of this product within the commercially available tools.

At the same time, the development of this new approach will also to be accompanied with the well-established and already in-solution validated tests. These enzymatic assays are already developed in the host laboratory, employing colorimetric methodologies^6,7.

We believe that proposed project is in line with the needs of the current suggestions of European directive 2025/2360 on soil monitoring and resilience⁸, as well as the growing need for innovative approaches based on field-based measurements of environmental indicators. 

The succesfull candidate will work under supervision of Dr. Jasna Nikolić Chenais and Dr. Thérèse de Caldas at the biochemical research platform Biochem-Env (UMR EcoSys, INRAE). The host laboratory is strongly dedicated to the environmental research, identifying and selecting biological indicators of ecosystem health, and developing innovative approaches for exploiting these indicators in the research. Biochem-Env is recognized as a leader platform in measuring enzymatic activities in the soil samples, and has expertises in biochemistry, bioanalytical measurements and chemistry of polysaccharides, that are neccessary for conducting the proposed project^9,10. Initially, the developed tools will be tested and used in the ongoing research projects of our collaborators within the unit UMR EcoSys. Later, these tools will be presented to the broather list of collaborators, including national and international research projects.

The successful Master 2 level candidate is expected to obtain or further strengthen their skills in soil sample preparation, enzymatic assays in solution and in-gel, scientific writing, and scientific communication.

Application instructions

The candidate is expected to have competences in biology, biochemistry and/or microbiology, with an interest in environmental sciences. Interested candidates are invited to submit their application including a CV and a motivation letter, to the following email address: contact-biochemenv@inrae.fr. The deadline for sending applications in October 20th, 2026.

Literature

1. Daunoras J, Kačergius A, Gudiukaitė R. Role of Soil Microbiota Enzymes in Soil Health and Activity Changes Depending on Climate Change and the Type of Soil Ecosystem. Biology (Basel). 2024;13(2):85. doi:10.3390/BIOLOGY13020085

2. Dick RP. Soil enzyme activities as indicators of soil quality 1. Defining Soil Quality for a Sustainable Environment. Published online October 26, 2015:107-124. doi:10.2136/sssaspecpub35.c7

3. Li D dan, Zhang Z, Wang J ning, Zhang P, Liu Y, Li Y zhong. Estimate of the degradation potentials of cellulose, xylan, and chitin across global prokaryotic communities. Environ Microbiol. 2023;25(2):397-409. doi:10.1111/1462-2920.16290

4. Talamantes D, Biabini N, Dang H, Abdoun K, Berlemont R. Natural diversity of cellulases, xylanases, and chitinases in bacteria. Biotechnology for Biofuels 2016 9:1. 2016;9(1):133-. doi:10.1186/S13068-016-0538-6

5. Nguyen STC, Freund HL, Kasanjian J, Berlemont R. Function, distribution, and annotation of characterized cellulases, xylanases, and chitinases from CAZy. Appl Microbiol Biotechnol. 2018;102(4):1629-1637. doi:10.1007/s00253-018-8778-y

6. Cheviron N, Grondin V, Nelieu S, et al. Biochem-Env, a platform of environmental biochemistry for research in ecology and ecotoxicology. Focus on Microscopy. 2014;(1):255. doi:10.34894/VQ1DJA

7. Cheviron N, Grondin V, Marrauld C, et al. Inter-laboratory validation of an ISO test method for measuring enzyme activities in soil samples using colorimetric substrates. Environmental Science and Pollution Research. 2022;29. doi:10.1007/s11356-021-17173-3ï

8. Directive - EU - 2025/2360 - EN - EUR-Lex. Accessed July 17, 2026. https://eur-lex.europa.eu/eli/dir/2025/2360/oj/eng

9. FOCUS PLATEFORME : Biochem-Env, plateforme lauréate de l’appel à manifestations d’intérêt « Data papers et Plateformes » de l’Université Paris-Saclay. doi:10.15454/HA6V6Y

10. Cheviron N, Grondin V, Mougin C. Biochem-Env: a platform of biochemistry for research in environmental and agricultural sciences. Environ Sci Pollut Res Int. 2018;25(7):6154-6157. doi:10.1007/S11356-017-8973-X