Chronic exposure to antibiotics and metals in soil : impact on microbial processes including antibiotic resistance dynamic – CEMABS

The intensive use of antibiotics in human and veterinary medicine, to protect plants and fruits, and to promote animal growth in livestock production facilities led, directly or through amendments, to the widespread dissemination of antibiotics in the environment. To cope with the toxic effect of antibiotic microorganisms have evolved many strategies leading to the emergence and spread of resistance genes among a wide range of microbial species and the increase prevalence of multidrug resistance. There is evidence of positive correlation between antibiotic consumptions/concentrations and resistance rates in high-antibiotic use/accumulation areas. Furthermore, some agriculture practices such as amendment with biofertilizers contribute to the dissemination of antibiotics, and thus various antibiotics have been detected in soil. Anthropogenic sources of antibiotics might contain several contaminants (i.e. several pharmaceuticals, metals) and can be associated to a complex organic matter that modifies contaminant properties. Similarly soils might already be contaminated with various chemicals as organic pesticides and metals that regularly enter in soil or have been accumulated through repeated treatments. These compounds are also known to alter microbial cell integrity and act as selective agents that can co-select for various resistances including antibiotic resistance. These phenomena have been reported for metals in diverse environments. Whether antibiotics in the context of the presence of other potential contaminants as metals have synergistic adverse effects on soil microbial communities and favour the emergence and spread of antibiotic resistance need to be further investigated. In addition, soils harbour an extent diversity of bacterial species including naturally antibiotic resistant populations. These bacteria are heterogeneously distributed in the soil matrix and then differently exposed to contaminants. Consequently risk assessment studies in soil are very complex and require considering both the way soil are exposed to and the specific intrinsic properties of soil. These parameters will strongly influence the dose, the availability and the length exposure of microbial communities and then their response. The objectives of this program are to evaluate whether the joint dispersal of antibiotics and metals, through chronic level exposure, would i) impact diversity and functions of microbial communities, ii) contribute to raise tolerance within bacterial communities and iii) lead to the emergence of new antibiotic resistance mechanisms. This will be addressed through a dose-response approach, taking into account parameters that will influence bioavailability and aiming at determining no/acceptable effect concentration regarding microbial processes, as a first step towards risk assessment. Also the timeframe of occurrence and the spatial distribution within the soil matrix will be investigated.
In particular, it will focus on i) the development of methods of extraction to quantify total and bioavailable antibiotic and metal concentration in soils, ii) on the analysis of their fate in term of transport (from top soil to groundwater), retention time, interaction with soil constituents but also in term of chemical and biological transformations iii) on the development and application of bioindicators of pollution induced tolerance (PICT) and, finally, iv) the dynamic of prevalence of antibiotic resistance phenotypes and antibiotic resistance genes.
It will rely on two complementary types of studies: in agricultural experimental fields and in controlled (lab) column systems. Agricultural fields have a short- or long-history of biofertilizer application, well described structural, physico-chemical and microbiological characteristics. In contrast, column equipments, where amendment history and intake will be controlled, will be set up to address the dose-response relationship as well as refined spatial considerations.