Human activities have affected the surrounding natural ecosystems, including belowground microorganisms, for millennia. Their short‐ and medium‐term effects on the diversity and the composition of soil microbial communities are well‐documented, but their lasting effects remain unknown. When unoccupied for centuries, archaeological sites are appropriate for studying the long‐term effects of past human occupancy on natural ecosystems, including the soil compartment. In this work, the soil chemical and bacterial compositions were compared between the Roman fort of Hegra (Saudi Arabia) abandoned for 1500 years, and a preserved area located at 120 m of the southern wall of the Roman fort where no human occupancy was detected. We show that the four centuries of human occupancy have deeply and lastingly modified both the soil chemical and bacterial compositions inside the Roman fort. We also highlight different bacterial putative functions between the two areas, notably associated with human occupancy. Finally, this work shows that the use of soils from archaeological sites causes little disruption and can bring relevant information, at a large scale, during the initial surveys of archaeological sites.

Forest ecosystem disturbances generate changes including soil changes, generally with loss of topsoil and loss of much of the diversity of microorganisms, which are usually replaced by others that are more adapted to the new conditions. We describe the effect of rainforest clear-cutting in Madagascar, with stripping of surface soil horizons among ectomycorrhizal fungal communities associated with natural Asteropeia mcphersonii seedlings. An experimental device was placed on four sites, each including an undisturbed plot with litter and a plot in clear-cut areas on a soil composed of a homogeneous mineral substrate. On each of these eight plots the ectomycorrhizal infection rate was determined and root tips were collected to sequence the internal transcribed spacer. 219 sequences grouped into 59 operational taxonomic units (OTUs) were obtained. The main taxonomic groups were Russulaceae, Boletales and Thelephoraceae. Marked spatial aggregation was observed for OTUs. The disturbance significantly affected the ectomycorrhizal infection rate of A. mcphersonii seedlings and the OTU composition of mycorrhizal communities. However, some OTUs were found in both types of environments. We discuss the effect of the disturbance on mycorrhizal communities associated with natural ectomycorrhizal A. mcphersonii seedlings, particularly in view of its application to ecological restoration of disturbed forest environments.