The "Biogeochemistry and Biotechnology" cluster combines FARE's technical skills in several fundamental disciplines for the study of microbial and enzymatic functioning in complex environments.

Biogeochemistry

The research programmes developed within this discipline involve experiments conducted in the field or under controlled laboratory conditions to study the fate of plant litter and organic matter in the soil, in relation to their chemical composition. They draw on skills in chemistry, microbiology, soil science and agronomy. This activity uses a range of technical resources to i) monitor the dynamics of nitrogen, carbon and soil microbial dynamics, ii) quantify and functionally characterise microbial communities (C and N of the microbial biomass, microbial diversity by analysing the fatty acids of the phospholipids of microbial cell membranes - PLFA, microbial respiration, mineralisation and enzymatic activities), iii) characterise the soil's hydric properties and iv) measure greenhouse gas emissions such as CO₂ and N₂O during the decomposition of plant litter in the soil or on the soil surface (mulch). 

Analysis methodes, measurements and equipments :

- Techniques for measuring gross flows of nitrogen mineralisation/organisation by ¹⁵N isotope tracing (dilution/isotope enrichment)
- ¹³C isotope tracing using ¹³C-enrichmed plant biomass
- Carbon and nitrogen from microbial biomass by fumigation-extraction
- Van Soest biochemical fractionation of litter by proximal analysis
- Nitrogen and Total Carbon, soluble carbon,in soils and plant litter
- ¹³C and ¹⁵N isotope analyses carried out by LADIS
- Enzymatic activities (β-1.4 Glucosidase, β-Xylosidase, Phenoloxydase, Peroxydase, L-Leucine aminopeptidase,...)
- Ergosterol in soil and litter
- Carbonates, nitrate, ammonium by segmented flow spectrophotometry
- Gaz flows (CO₂, N₂O) by infra-red spectroscopy
- Soil moisture measurment (EC capacitif sensors)
- Water potential (pF) - soil moisture curve (Richards presses)
- Measurement of climatic variables (mobile weather stations) to calculate potential evapotranspiration (global solar radiation, relative humidity, anenometer, temperature, rain fall)
- Laboratory rainfall simulators (intensity, duration)                                                                                    - Measurement of soil bulk density (rings, membrane volumeter)

Biotechnology

The UMR's AFERE -Agroressources FERmentation Enzymes Chair has a wide range of skills and equipment for implementing white biotechnology processes to fractionate and transform plant biomass.

1.Microbiology-fermentation 

- Cultures of aerobic and anaerobic micro-organisms; bacteria and fungi (yeasts, rots and basidiomycetes); isolated cultures, co-cultures, consortia.
- fermentation in liquid medium (MLF) and solid medium (SMF).
- Bioproduction of enzymes and microbial secondary metabolites (pigments, etc.). Extraction and quantification of fermentation products.
- Measurement of micro-organism respiration (FMS)
- Testing of prebiotic properties and antimicrobial tests.

Equipments : laminar flow hoods and PSM, microscopes, incubators, MLF bioreactors FML (from a few mL to 5L and 20L), FMS columns (50 to 300 g), FMS bioreactor (1-20 kg), anaerobic chamber (<0,1ppm O₂), HPLC.

2.Molecular biology

- Cloning, heterolous expression of bacteria and yeats, directed mutagenesis, study of the dynamics, activity and diversity of microbial communities.
- Genomic, transcriptomic, proteomic and bioinformatics analyses.

Equipments : thermal cyclers, qPCR, electrophoresis equipment, etc.

3.Biocatalysis

- Production and purification of enzymes (cellulases, hémicellulases, pectinases, oxydo-réductases). 
- Enzyme characterisation (enzymatic activity, kinetic parameters, pH and temperature stability).
- Immobilisation of enzymes.
- Enzyme catalysis with pure enzymes or in cocktails
- Biocatalytic hydrolysis, transglycosylation, (trans)esterification and oxidation-reduction reactions.
- Enzymatic fractionation of plant biomass into sugars (monosaccharides, oligosaccharides), phenolic molecules.
- Enzymatic synthesis of glycosides, alkyl glycosides, sugar esters, phenolic esters.
- Bio-electrocatalysis, design de bio-electrodes operating with oxidoreductases involved in the fractionation of lignocellulosic biomass.
- Purification and quantification of reaction products.

Equipments : stirring-mixing reactors from 50 mL to 2L, visible-UV-fluorescence microplate readers, thermostatic spectrophotometers, HPLC.