Khawla Lazrak

• Many dryland and desert rivers, especially in North Africa, faced significant physicochemical and hydromorphological extreme changes due to climate change and anthropogenic pressures such as agriculture, mining, and tourism. These impacts are increasing the concentration of salts, threatening biodiversity, freshwater ecosystem functions and services, and raising vulnerability to water quality degradation, water security, and human wellbeing. While freshwater salinization is an escalating concern, understanding its effects on intermittent rivers and ephemeral streams (IRES) in the arid North Africa region is still limited and receives little scientific attention. The Drâa river (southeastern Morocco) is a humanregulated river facing multiple human pressures, resulting in reduced flow and increased water salinity. The main objective of this thesis is to investigate the composition, diversity, structure, and dynamics of benthic microalgae communities in the arid Drâa river, examine their responses to salinization effects, and assess water quality and ecological status using morphological versus molecular metabarcoding approaches. The results showed that salinity increases from the upper to the lower Drâa, rising during dry periods due to reduced water flow and increased evaporation. Benthic microalgae samples from 19 sites during dry and wet periods revealed an important diversity of 159 diatom species, 40 green algae, and 48 cyanobacteria species identified morphologically. The morphological and DNA metabarcoding analysis of the benthic microalgae community reveals that salinity and hydrological conditions greatly affect their assemblages and composition, particularly for diatoms, with salinity emerging as the major influencing factor. Examining water quality index through physicochemical parameters revealed that mineralization (conductivity and chloride) affects the lower and middle Drâa, while other factors influence the upper Drâa. This upstream part of the basin faced less pollution than the middle and lower Drâa, which are more impacted by anthropogenic pressures. The water quality index indicated worse values in the lower Drâa due to high point source pollution, while the IPS diatom index highlighted its reliability in capturing long-term environmental changes in the river. The diatom index IPS values from classical morphological and DNA metabarcoding analysis significantly correlated with similar ecological quality classes for over half of the samples, despite varying taxonomic compositions. The biofilm field-transfer experiment demonstrated that increasing salinity in the Drâa river negatively affects benthic microalgae, both in terms of biomass and diversity, while lower salinity in brackish areas can benefit their growth. Similarly, the freshwater biofilm of the Drâa river was exposed to different salinity levels (1, 10, 30 g/L NaCl) using a microcosm experiment, demonstrating physiological and biochemical changes in response to salt stress for survival. Low salinity levels (1 g/L) promote biofilm development, whereas higher levels (10 and 30 g/L) hinder it. More specifically, the experimental batch culture evaluated the impact of increasing salinity on two diatom strains isolated from different salt habitats, showing that the halotolerant diatom species have greater physiological plasticity at higher salinity than the freshwater diatom strains. The thesis results will enhance the understanding of the ecological impacts of freshwater salinization on benthic microalgal communities, predicting the consequences on aquatic ecosystem services, water quality, and implementing monitoring schemes, mitigation measures, and best management practices. These findings highlight the effectiveness of benthic diatoms as bioindicators for arid and desert river water quality and ecological assessments using both microscopic and molecular techniques.