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. Endolithic microhabitats have been described as the lastrefuge for life in arid and hyper-arid deserts where life has to deal withharsh environmental conditions. A number of rock substrates from thehyper-arid Atacama Desert, colonized by endolithic microbial communitiessuch as halite, gypsum crusts, gypcrete, calcite, granite and ignimbrite,have been characterized and compared using different approaches. In thiswork, three different endolithic microhabitats are described, each one witha particular origin and architecture, found within a lithic substrate knownas gypcrete. Gypcrete, an evaporitic rock mainly composed of gypsum(CaSO 4 ⋅  2H 2 O) and collected in the Cordon de Lilaarea of the desert (Preandean Atacama Desert), was found to harbourcryptoendolithic (within pore spaces in the rock), chasmoendolithic (withincracks and fissures) and hypoendolithic (within microcave-like pores in thebottom layer of rock) microhabitats. A combination of microscopy investigationand high-throughput sequencing approaches were used to characterize theendolithic communities and their habitats at the microscale within the samepiece of gypcrete. Microscopy techniques revealed differences in thearchitecture of the endolithic microhabitats and the distribution of themicroorganisms within those microhabitats. Cyanobacteria and Proteobacteriawere dominant in the endolithic communities, of which the hypoendolithiccommunity was the least diverse and hosted unique taxa, as a result of lessaccess to sun radiation. These results show, for the first time, that thedifferences in the architecture of a microhabitat, even within the samepiece of a lithic substrate, play an essential role in shaping thediversity and composition of endolithic microbial communities.

The composition of endolithic communities in gypcrete is determined by the specific microhabitat architecture