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Over the last decades, global warming has increasingly stimulated the expansion of cyanobacterial blooms in freshwater ecosystems worldwide, in which toxic cyanobacteria produce various congeners of cyanotoxins, mainly dominated by microcystins (MCs). MCs introduced into agricultural soils have deleterious effects on the germination, growth and development of plants and their associated micro-biota, leading to remarkable yield losses. Phytotoxicity of MCs may refer to the inhibition of phosphatases activity, generating deleterious reactive oxygen species, altering gene functioning and phytohormones translocation within the plant. It is also known that MCs can pass through the root membrane barrier, translocate within plant tissues and accumulate into different organs, including edible ones. Also, MCs impact the microbial activity in soil via altering plant-bacterial symbioses and decreasing bacterial growth rate of rhizospheric microbiota. Moreover, MCs can persist in agricultural soils through adsorption to clay-humic acid particles and results in a long-term contact with the plant-microflora complex. However, their bioavailability to plants and half-life in soil seem to be influenced by biodegradation process and soil physicochemical properties. This review reports the latest and most relevant information regarding MCs-phytotoxicity and impact on soil microbiota, the persistence in soil, the degradation by native microflora and the bioaccumulation within plant tissues. (C) 2019 Elsevier Ltd. All rights reserved.