Porous media have been found to remove bacterial pathogens from polluted infiltrating water by a combination of physical and biogeochemical processes. Physically, they are removed by size-exclusion processes; geochemically, they absorb to soil surfaces; biogeochemically, their fate is associated with biofilm formation, composition and growth.
Bioﬁlms are communities of microorganisms that are attached to surface grains and embedded within a matrix consisting of extracellular polymeric substances (EPS) composed of proteins, polymers, and DNA material. When pathogens reach the area colonized by biofilms, a competition with indigenous bacteria is stablished, and pathogens eventually integrate into biofilms, as a way to decrease predation effects. This way, bacteria get stuck close to the entry point (latrines, dead animals, wastewater disposal), and porous media behaves as a natural effective filter. No physical complete model is yet available to study this topic of fate of pathogens in a bio-amended soil including competition of native bacteria, pathogens, in a biofilm colonized soil.
Despite all the work published in the literature, there are still quite a number of open challenges or questions:
1) It has been found that bacterial pathogens do not travel (much), strongly filtered by porous media; on the other hand, (ground)waterborne diseases caused by bacterial pathogens (cholera, dysentery) spread even in countries with high sanitation standards. This is an unresolved contradiction.
2) The concept of bacteria deactivation is not yet well understood. Do they really degrade and lose their pathogenic effect, or just get stuck in the biofilm, with the potentiality to be released to the system anytime?
3) What is the interaction between pathogens and biofilm? What is the role of EPS on bacterial fixation and removal?
Most of the processes occurring at the porous level are unknown. Biofilms can have very different shapes, and these shapes have not yet been related to physico-chemical properties: porous networks, nutrients loads, …
Studying such a complex biogeochemical system requires not only the identification and quantification of relevant processes important to different disciplines but mostly the study of interactions among them. Along this line, it is necessary to produce small- and intermediate-scale lysimeter experiments at the laboratory aimed at studying: (i) how the infiltration rate is modulated in time by bacterial activity, and (ii) how physicochemical changes and biological activity interact and change spatially and temporally.
This line involves two approaches to modeling: conceptual and numerical. Regarding the former, we discriminate the driving processes and write the governing equations of transport over multiple scales. The discretization of a numerical model is usually larger than the spatial resolution required to model such processes. This calls for the necessity to use effective or upscaled models formally derived.
All the models developed are incorporated into a numerical model based on fully Lagrangian methods, as they offer convenient and efficient solutions when dealing with heterogeneities and a variety of complex transport processes. These methods simulate solute transport by tracking in time a large number of particles injected into the system, representing the different species tracked (here bacteria, dead or alive, pathogenic or not, and EPS at least, but also algae, enzymes,…). The state, position, and mass of the particles are changed according to predefined relationships representing the actual processes occurring. Activation and deactivation of bacteria is controlled by simple statistical rules.