The effect of vegetation and environmental variables on microbial community composition differed among the three microbial domains investigated. Fungal community dissimilarity patterns were related to SOM, which is in line with the typical saprophytic status of most of Fungi and their higher competitiveness for complex substrates compared to Bacteria The observed SOM effect on fungal communities may be direct, but may also reflect the recruitment of different mycorrhizal association type in ecosystems displaying contrasted SOM and nutrient cycles. Indeed, ericoid- and ectomycorrhizal associations are usually more occurrent in ecosystems with lower SOM recycling. Crenarchaeal communities were not affected by SOM, which supports the idea that many soil Crenarchaeas are autotrophic ammonia oxidizers. This may also explain the lack of creanarchaeal community covariation with annual radiation compared to bacterial and fungal communities. Indeed, annual radiation is a decisive factor for plant growth and growing season length that strongly impacts on plant community composition, nutrient conservation strategy, and therefore on soil resources. In contrast, annual radiation did not covaried with soil water content at the sampling time, excluding an immediate effect of water availability on the observed patterns. Both cases suggest a direct or indirect effect mediated by plant communities on bacterial and fungal communities. In general, soil pH appeared to be a good predictor for microbial community composition as reported Ac-YVAD-pNA previously. For Crenarchaeota, Nicol et al. observed that different creanarchaeal lineages occurred in soils with pH that varied by 2.5 units. In our study, crenarchaeal 16S RNA genes were hardly PCR-amplifiable in the most acidic soils. In contrast, bacterial and fungal PCR amplifications were possible for these Perlapine samples, which suggests a possible detrimental effect of low pH on crenarchaeal populations. The significant covariation between pH and bacterial diversity may be related to Acidobacteria, a dominant group of soil Bacteria known to be highly responsive to soil pH.