10Vadose zone oxygen dynamics control all subsurface redox reactions and play a decisive role in 11 maintaining groundwater quality. Although drying and wetting events are common in artificial 12 recharge, their effects on subsurface oxygen distribution are poorly documented. We monitored 13 oxygen concentration in the unsaturated zone in a mid-scale (1 m high) laboratory soil lysimeter, 14which was subjected to short wetting and drying cycles that simulated a highly permeable 38• Surface scraping results in an immediate but temporary increase in the infiltration rate 39• Quantifying small changes in space and time is vital for accurate pore-scale O 2 mapping 40 3

17Water flowing through hyporheic river sediments or artificial recharge facilities promotes the 18 development of microbial communities in depth. We performed an 83-day mesocosm

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This is the peer reviewed version of the following article: [Carles Brangarí, A., X. Sanchez-Vila, A. Freixa, A. M. Romaní, S. Rubol, and D. Fernàndez-Garcia (2017), A mechanistic model (BCC-PSSICO) to predict changes in the hydraulic properties for bio-amended variably saturated soils, Water Resour. Res., 53, 93–109, doi:10.1002/2015WR018517], which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1002/2015WR018517/abstract. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.The accumulation of biofilms in porous media is likely to influence the overall hydraulic properties and, consequently, a sound understanding of the process is required for the proper design and management of many technological applications. In order to bring some light into this phenomenon we present a mechanistic model to study the variably saturated hydraulic properties of bio-amended soils. Special emphasis is laid on the distribution of phases at pore-scale and the mechanisms to retain and let water flow through, providing valuable insights into phenomena behind bioclogging. Our approach consists in modeling the porous media as an ensemble of capillary tubes, obtained from the biofilm-free water retention curve. This methodology is extended by the incorporation of a biofilm composed of bacterial cells and extracellular polymeric substances (EPS). Moreover, such a microbial consortium displays a channeled geometry that shrinks/swells with suction. Analytical equations for the volumetric water content and the relative permeability can then be derived by assuming that biomass reshapes the pore space following specific geometrical patterns. The model is discussed by using data from laboratory studies and other approaches already existing in the literature. It can reproduce (i) displacements of the retention curve toward higher saturations and (ii) permeability reductions of distinct orders of magnitude. Our findings also illustrate how even very small amounts of biofilm may lead to significant changes in the hydraulic properties. We, therefore, state the importance of accounting for the hydraulic characteristics of biofilms and for a complex/more realistic geometry of colonies at the pore-scale.Peer ReviewedPostprint (author's final draft