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Desert regions and arid soils are stabilized by a crust of cyanobacteria that bind sand to extruded polysaccharides. In these environments, cyanobacteria lie dormant during most of the year, but photo-synthesize immediately when seasonal rains fall to take advantage of limited water resources. Desert cyanobacteria in biological soil crusts are known to produce a variety of toxins including microcystins and beta-N-methylamino-L-alanine (BMAA). We tested the hypothesis that toxin production of biological soil crusts increases directly following rainfall in arid environments. In the deserts of Qatar, meter square quadrats were divided into four treatment regimes: 1) intact crust; 2) watered intact crust; 3) disturbed crust; 4) watered disturbed crusts. Five replicates of each quadrat were monitored and tested for chlorophyll a as well as for the presence of three cyanobacterially-produced toxic isomers BMAA, 2,4diaminobutyric acid (DAB), and N-(2-aminoethyl)glycine (AEG). Median chlorophyll content of soil samples from sections of the quadrats that were mechanically disturbed was only 37% of the chlorophyll a content from undisturbed sections, but neither watering nor disturbance had a significant impact on toxin content. These results suggest that low molecular weight cyanotoxins produced by biological soil crusts are persistent in the environment, and can survive even the removal of the crusts themselves. Thus, over many years a potentially large reservoir of cyanobacterial toxins can accumulate in desert soils, with possible health consequences for human exposure to particulate matter in dust storms, and from disturbance of desert soils from construction activities and military activities that result in loss of soil structure. Mechanical disturbance of either surface or below surface on dry or wet soils may equally contribute to human exposure to cyanotoxins through inhalation. (C) 2014 Elsevier Ltd. All rights reserved.