Impact of viral and phage populations in soil-percolating methanization products ? food matrices continuum

Description: Employer organisation The internship will be realized in two laboratories located at Dijon, France UMR PAM The PAM Lab plays a major role in scientific and technological advances in the field of food and wine. The joint scientific focus of all the members is to understand the physical, chemical, and biological phenomena that determine food quality with the ambition of developing new products and new food processes. The PAM Lab is composed of 4 research teams: ? Microbiological and Biotechnological Processes (PMB) ? Physico-chemistry of Food and Wine (PCAV) ? Food Wine Microbiology and Stress (VAlMiS) ? Food Biotech&Innovation (FBI) The PAM Lab is in charge of three technical facilities: RMB (Rheology of Biological Materials), PIMS (Spectroscopic and Microscopy Imaging) and Oenoviti (Wine studies) It is a member of the Carnot Institute Qualiment®, national center of excellence for the promotion of research in the food industry. UMR Agrécologie The developed researches lead in the Agroecology Joint Research Unit help to understand the biotics interactions particularly those between plants to plants and between plants to microorganisms. The analysis focuses on agrosystems with the aim to design innovative and environment-friendly systems. In that way, the developed researches answer two major stakes: Analyze, understand and act on the interactions and regulations within communities with various spatial and temporal scales; Offer innovative systems of cultures to ensure a good agricultural production in sufficient amount, while respecting the environment Description Viruses are non-living biological entities found in water, soil and air. Artificial environments such as those in the food and pharmaceutical industries are also concerned. When managing waste in the environment, bacteriophages are found both in wastewater and in recycled products from the sector such as, for example, percolates from anaerobic digestion and methanization (Batinovic et al., 2019; Haq et al., 2012; Kleppen et al., 2011; Po?aska and Soko?owska, 2019; Swanson et al., 2009). Phages (viruses capable of infecting bacteria) are considered to be the most abundant biological entities in the biosphere with around 1031 particles present, i.e. 10 times more than bacteria (Batinovic et al., 2019; Mann, 2005).In the soil, around 109 viral particles are counted per gram of dry matter, the virus / bacteria ratio being very dependent on the characteristics of the soil (Swanson et al., 2009; Witzany, 2011). Between 108 and 109 viral particles are also counted per milliliter of water from wastewater treatment plants (Otawa et al., 2007).During anaerobic digestion processes (methanization), the behavior and role of phages / viruses as well as their fate in soils remain poorly understood (Heyer et al., 2019; Smith et al., 2015; Baert et al., 2010; Lund et al. ., 1996).In the food industry, phages are an alternative to antibiotics and can be tools for fighting against spoilage or pathogenic bacterial flora (phage therapy) (Christiansen et al. 2014; Hagens and Loessner, 2014). Conversely, certain pathogenic viruses for humans such as noroviruses (NoV), rotaviruses (HRV) and hepatitis A and E viruses can contaminate water and foodstuffs and therefore constitute a real public health threat (Pal and Ayele, 2020). The viral load in foods of these human pathogenic viruses is low, for example 2.103 NoV particles are counted per gram of oyster on average (Hunt et al. 2020). However, a wide variety of food matrices are likely to be contaminated by these viruses: seafood, meats, fruits and vegetables for example (Pexara and Govaris, 2020). Although they are likely the most prevalent organisms in the biosphere, the litterature relating to the nature and role of viruses in the dynamics of bacterial populations and their impact on natural (soil) or anthropized (methanization percolate, food) environments is scarced and very fragmented (Calero-Cáceres et al., 2019; Ross and Topp, 2015; Salmond and Fineran, 2015; Trubl et al., 2018; Braga et al., 2020; Göller et al., 2020; Hrdy et al. , 2021). This is partly due to the technical issues encountered by these studies. Indeed, the main limits for the analysis of viral loads in complex environments (soil, percolating methanization products, food, for example) are due to : i) the composition of the matrices which, depending on their physicochemical nature, can drastically reduce virus extraction yields and inhibit gene amplification reactions,ii) the small amounts of virus found in certain matrices, in particular food,iii) the difficulty in evaluating the infectivity of viruses or phages due to the lack of identifiedrecipient host cells. Objective:In light of this observations, it appears necessary to adapt the methods of extraction and detection of virus/bacteriophages to complex matrices, to optimize them in order to quantify very low viral/phage loads and finally to analyze the virome/phagome of these matrices. Methods: A-Setup, optimization of viral extraction procedures and quantification of viral load from various matricesThe bacteriophage MS2 specific to Escherichia coli K12 Hfr+ will be used as a model. It will be spread in the following matrices at different concentrations:* Liquid milk*E. coli growth medium (LB)*Soil matrix*Methanization product Different extraction procedures will be tested and optimized during the internship to recover the MS2 phage from these matrices. The viral load will be assessed by both the plaque forming colonies (PFU) method (using E. coli K12 Hfr as host) and by a molecular method i.e. RNA extraction followed by digital droplet PCR using specific primers and probe. B-Virome evaluation from various matricesEndogenous viruses and phages extracted in part A from samples of milk, soil, methanization products will be analyzed by the means of the Next Generation Sequencing (NGS) - Shotgun method to describe and characterize new viral populations from the various matrices analysed. This approach will be completed with the PFU method in the case of phages to get phage/bacterium couples. Profile The candidate must have skills in the field of microbiology (or virology) and molecular biology and have an should be interested by the virology. Starting date Dès que possible