Know more

About cookies

What is a "cookie"?

A "cookie" is a piece of information, usually small and identified by a name, which may be sent to your browser by a website you are visiting. Your web browser will store it for a period of time, and send it back to the web server each time you log on again.

Different types of cookies are placed on the sites:

  • Cookies strictly necessary for the proper functioning of the site
  • Cookies deposited by third party sites to improve the interactivity of the site, to collect statistics

Learn more about cookies and how they work

The different types of cookies used on this site

Cookies strictly necessary for the site to function

These cookies allow the main services of the site to function optimally. You can technically block them using your browser settings but your experience on the site may be degraded.

Furthermore, you have the possibility of opposing the use of audience measurement tracers strictly necessary for the functioning and current administration of the website in the cookie management window accessible via the link located in the footer of the site.

Technical cookies

Name of the cookie


Shelf life

CAS and PHP session cookies

Login credentials, session security



Saving your cookie consent choices

12 months

Audience measurement cookies (AT Internet)

Name of the cookie


Shelf life


Trace the visitor's route in order to establish visit statistics.

13 months


Store the anonymous ID of the visitor who starts the first time he visits the site

13 months


Identify the numbers (unique identifiers of a site) seen by the visitor and store the visitor's identifiers.

13 months

About the AT Internet audience measurement tool :

AT Internet's audience measurement tool Analytics is deployed on this site in order to obtain information on visitors' navigation and to improve its use.

The French data protection authority (CNIL) has granted an exemption to AT Internet's Web Analytics cookie. This tool is thus exempt from the collection of the Internet user's consent with regard to the deposit of analytics cookies. However, you can refuse the deposit of these cookies via the cookie management panel.

Good to know:

  • The data collected are not cross-checked with other processing operations
  • The deposited cookie is only used to produce anonymous statistics
  • The cookie does not allow the user's navigation on other sites to be tracked.

Third party cookies to improve the interactivity of the site

This site relies on certain services provided by third parties which allow :

  • to offer interactive content;
  • improve usability and facilitate the sharing of content on social networks;
  • view videos and animated presentations directly on our website;
  • protect form entries from robots;
  • monitor the performance of the site.

These third parties will collect and use your browsing data for their own purposes.

How to accept or reject cookies

When you start browsing an eZpublish site, the appearance of the "cookies" banner allows you to accept or refuse all the cookies we use. This banner will be displayed as long as you have not made a choice, even if you are browsing on another page of the site.

You can change your choices at any time by clicking on the "Cookie Management" link.

You can manage these cookies in your browser. Here are the procedures to follow: Firefox; Chrome; Explorer; Safari; Opera

For more information about the cookies we use, you can contact INRAE's Data Protection Officer by email at or by post at :


24, chemin de Borde Rouge -Auzeville - CS52627 31326 Castanet Tolosan cedex - France

Last update: May 2021

Menu Logo Principal logo SOERE PRO Logo CIRAD Logo AnaEE Logo IRD Logo Ouagadougou university

Home page

Occurrence of pathogens in soils and plants in a long-term field study regularly amended with different composts and manure

V. Brochier (a), P. Gourland (a), M. Kallassy (b), M. Poitrenaud (a), S. Houot (c)

Brochier & al., 2011
Brochier & al., (2011), Agriculture, Ecosystems & Environment Volume 160, 2012, Pages 91-98

In order to protect soil and plant quality, the agronomic efficiency and hygienic safety of organic waste product (OWPs) amendments must be demonstrated prior to their application on cultivated fields. Indeed, the application of OWPs to agricultural land without control of their hygienic safety is one potential route by which pathogens may enter the human food chain [1]. Pathogens can be present in raw materials like organic wastes, sewage sludge or in livestock manures. However, the composting process, when it is properly managed, reduces pathogen levels [2]. This study evaluates the potential microbial contamination of soil and crops of maize and wheat after compost or manure application in a long-term field experiment.

Main results

Organic amendments or fertilizers are valuable sources of nutrients for plants and organic matter, contributing to soil quality and fertility. Recycling of organic waste products to agricultural land is considered as being one of the most economical, practical and environmentally beneficial management options[1]. Survival of pathogens in soil or their potential transfer to plants after livestock or sewage sludge application has been described in some studies [2]. In contrast, few works concern the fate of pathogens after compost application [3]. In addition, most studies deal with inoculated organic materials, with large amounts of pathogens, which is not representative of realistic agricultural practices.

The aim of our study was to evaluate the potential microbial contamination and its evolution in soils and crops (corn and wheat) after compost or manure application of soil and crops (maize and wheat) after using realistic agricultural practices, in a long-term field experiment. This apprehension of the micro-organisms destiny that are signatories of contamination distinguishes our study from those already carried out. In addition to the presence of pathogens in post-application soils, we count organisms that indicate the quality of the composting process. Finally, our study was conducted as part of a long-term field experiment, more faithful to current agricultural practices.

The field experiment, located at Feucherolles in France, 35 km west of Paris and started in 1998, consists of 5 organic treatments: soil amended with a biowaste compost (BIO), a municipal solid waste compost (MSW), a green waste and sewage sludge compost (GWS) and a farmyard manure (FYM) as the reference amendment, and non-amended soil as the control. Pathogens (Salmonella, Listeria monocytogenes, helminths eggs) and indicators of composting treatment efficiency (Escherichia coli, Clostridium perfringens, Enterococcus) were monitored as defined in the French compost standards. Enterococcus and C. perfringens were respectively quantified in organic amendments at the following orders of magnitude: 103–106 MPN g−1 and 10–103 CFU g−1, in accordance with the French standards. The other microorganisms were absent or below detection limits. Enterococcus and C. perfringens were respectively detected in soils at the following orders of magnitude: 102–103 MPN g−1 and 10–102 CFU g−1, without significant differences between amended and non-amended soils before and 34 months after spreading (figure 1).

Fig.1A Brochier
Fig.1B Brochier

Figure 1 : Contents of C. perfringens and Enterococcus in soils, values = means of 3 or 4 replicates at each date, error bars = standard deviation, values with the same letter are not significantly different according to the non-parametric Kruskal–Wallis Test (P < 0.05). Greys arrows mean spreading events.

Enterococcus levels were quite constant over time. However, temporal variations were observed for C. perfringens. Helminth eggs were rarely detected (in 11 of 50 soil samples), their presence showing no correlation with treatments and no persistence over time. The microorganisms were also looked for in wheat and maize. Plants were analyzed separately for stems + leaves, grains and roots. Enterococcus was detected in roots, stems + leaves and grains, at levels in the order of magnitude of 103–104 MPN g−1, without differences between the treatments. The lowest contents were found in grains. C. perfringens and helminths eggs were observed in roots, but they were not detected in grains. Levels of C. perfringens in roots were lower than 15 CFU g−1. Helminths eggs were frequently detected in roots, but rarely in stems + leaves. The other microorganisms were never detected in any parts of plants. In conclusion, for the studied microorganisms and with the analytical methods used, these results showed that the utilization of organic amendments compliant with French standards does not cause negative sanitary impacts on soil and plants.


1. Nicholson, F.A., Groves, S.J., Chambers, B.J., 2005. Pathogen survival during livestock manure storage and following land application. Bioresource Technology 96, 135–143.

2. Pourcher, A.M, Picard-Bonnaud, F., Ferré, V., Gosinska, A., Stan, V., Moguedet, G., 2007. Survival of faecal indicators and enteroviruses in soil after land-spreading of municipal sewage sludge. Applied Soil Ecology 35 (3), 473–479.

3. Wolna-Maruwka, A., Czekala, J., 2007. Dynamics of changes in the number of selected microorganism groups in sewage sludge and in manure subject to composting process and in the soil enriched with composts. Archive of Environmental Protection, Archiwum Ochrony Srodowiska 4, 53–66.


a Veolia Environment Research & Innovation, 291 av Dreyfous Ducas, F-78520 Limay, France

b Veolia Environmental Services, F-92000 Nanterre, France

c INRA, UMR Environment and Arable Crops, F-78850 Thiverval-Grignon, France