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Arid and semiarid crusted ecosystems occupy a large extent of the Earth’s surface. In these ecosystems there is a delicate balance between C sequestration and biodegradation that could easily be altered due to human disturbance or global warming. These environments are characterized by the presence of biological soil crusts (BSCs) coexisting with shrubs in the interspaces. BSCs play an important role in the C-cycle in arid and semiarid areas, but there has been little research regarding C-storage in crusted soils. In this research, representative BSCs were studied in three different crusted semiarid ecosystems in Southern Spain. Chemical fractionation and characterization of the organic matter in BSCs and underlying soils were undertaken to compare the total amount and quality of humic substances and find surrogate indicators of the soil organic matter quality. After isolating the major organic fractions (particulate fraction, humic acid-like (HA) and fulvic acid (FA)), the macromolecular, HA fraction was studied by derivative visible spectroscopy and resolution-enhanced infrared (IR) spectroscopy. Our results show quantitative differences in organic matter fractions, in agreement with the structural characteristics of the HA-type substances. The more stable crusted ecosystem with more evolved vegetation cover tend to be associated with HAs with broadband IR profiles, high optical density and macromolecular condensation and presence of polycyclic fungal biomarker compounds. In contrast, in the crusted ecosystem with very low or almost absent vascular vegetation cover, the C sequestration depends almost exclusively on the activity of crust-inhabiting organisms. It is suggested that the organic matter in BSCs shares characteristics with aquatic humic matter derived from non-lignified plants, including structurally complex HA-type substances which may have been originated by abiotic condensation of unsaturated lipids and/or diagenetic alteration of aliphatic biomacromolecules. Although these humification mechanisms have not been extensively studied in terrestrial soils they may be very active mechanisms for C sequestration in some types of crusted ecosystems. In particular, the spectroscopic characteristics in the visible and IR ranges of the crust-isolated HA-type substances provide the above-indicated biogeochemical proxies informing on the organic matter stability and quality and their bearing on the potential of crusted ecosystems for maintaining their properties after external disturbance. (C) 2012 Elsevier B.V. All rights reserved.