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In Mediterranean ecosystems, the soil biological crust (hereafter biocrust) plays a crucial role in maintaining ecosystem functioning. In these ecosystems, soil water content can often be a stronger driver of soil CO2 efflux than soil temperature, or at least comparable. However, little is known on the contribution of the biocrust to soil CO2 efflux or how the respiration of the biocrust responds to soil water content and temperature. A manipulative experiment was performed in a Mediterranean shrubland ecosystem in Sardinia (Italy) to assess the contribution of the biocrust to soil CO2 efflux and to identify the main environmental drivers of the CO2 efflux. For 19 months, in situ soil CO2 efflux was measured over two different surfaces: soil deprived of biocrust (hereafter Soil) and intact soil (hereafter Soil + BC), and estimated by subtraction in a third surface: biocrust (hereafter BC). CO2 efflux emitted by Soil, BC and Soil + BC was uniquely driven by soil moisture and temperature: BC respiration was mainly controlled by soil moisture at 5 cm depth, whereas both soil temperature and water content at 20 cm depth determined Soil CO2 efflux. Soil temperature and water content at 5 cm depth drove Soil + BC respiration. We also found that biocrusts can contribute substantially (up to 60%) to the total soil respiration depending on its moisture content. This contribution persists even in periods in which deeper soil layers are inactive, as small water pulses can activate the metabolism of carbon in soils through lichens, mosses and cyanobacteria associated with the biocrust, while deeper soil layers remain dormant. The important differences observed in CO2 efflux between Soil and Soil + BC suggest that carbon models and budgets may underestimate soil CO2 efflux in spatially heterogeneous Mediterranean areas. Our results highlight the importance of accounting for the biocrust contribution to soil respiration and its response to environmental drivers. We provide an accurate estimation of this key component of the carbon cycle at the ecosystem level in water limited ecosystems. (C) 2016 Elsevier B.V. All rights reserved.