Soil microbial communities are a major component of the biosphere and play a critical role in nutrient cycling and ecosystem functioning (van der Heijden et al., 2008). Consequently, identifying the key factors that control their composition is of great interest. The recent development of molecular tools has permitted a more thorough study of these communities. Abiotic factors such as soil pH and soil nutrient availability have been identified as key determinants of the richness and composition of microbial communities (Fierer and Jackson, 2006; Lauber et al., 2008). The changes in these factors along elevation gradients have been shown to drive compositional changes in microbial communities (Bryant et al., 2008; Fierer et al., 2011; Singh et al., 2012; Wang et al., 2012). In addition, single plant affects the composition of soil microbial communities (Kowalchuk et al., 2002) and plant cover is known to be a central driver of the spatial distribution of soil microorganisms (Eskelinen et al., 2009; Zinger et al., 2011). This status could result from the direct effect of species-specific mutualistic associations (Berg and Smalla, 2009; Hartmann et al., 2009) or from an indirect effect, as plants influence the physico-chemical properties of soil through litter deposition and root exudation of organic compounds (Eviner and Chapin, 2003; Bais et al., 2006). Despite recent insights into the biotic and abiotic factors affecting microbial communities (Zinger et al., 2011), three main issues impede our understanding of the underlying processes: (i) the complexity of the systems that are typically surveyed, which often involve multiple plant species and mature soils; (ii) the strong connection between soils and plant characteristics; and (iii) the lack of comparative analyses along environmental gradients that would allow us to assess how ecological processes can be affected by changes in abiotic variables.

We propose that cushion plants are an ideal model to simultaneously address these limitations and better understand how the interactions between biotic and abiotic factors may structure soil microbial communities. Cushion plants are a common growth form in alpine ecosystems (Körner, 2003) and provide a natural system with three main characteristics: (i) they are single or very dominant plants in a highly mineral matrix and can be seen as unique fertility hotspots in the desert, particularly in rocky landscapes with alpine cliffs where plant cover is very sparse or non-existent (Körner, 2003); (ii) they present a de novo soil formation resulting solely from the accumulation of its own living and dead tissues, thus reducing the confounding effect of other carbon sources that occur in mature soils; and (iii) they are broadly distributed along strong environmental gradients (e.g., elevation, bedrock). High mountain environments are characterized by low air and soil temperatures, high levels of solar radiation and wind exposure and strong effects on biotic communities (Körner, 2003). Consequently, cushion plants can be studied across broad altitudinal gradients to better understand how temperature and other associated abiotic factors that change with elevation can influence community and ecosystem properties. For these reasons, cushion plants have been extensively studied to determine how a single organism may modify local habitat conditions with consequences for the distribution and performance of other organisms. This type of non-trophic ecological interaction that strongly affects the community structure is referred to as ecosystem engineering (Jones et al., 1994, 1997). The low, compact stature and thick canopy of cushion plants is known to buffer temperatures and increase nutrient availability and water content compared to adjacent open areas (Arroyo et al., 2003; Cavieres et al., 2007; Yang et al., 2010; Anthelme et al., 2012). They are known to positively affect the richness of local plant (Badano et al., 2002; Arroyo et al., 2003; Badano and Cavieres, 2006; Cavieres et al., 2006; Antonsson et al., 2009; Sklenar, 2009; Yang et al., 2010; Anthelme et al., 2012; Molenda et al., 2012) and arthropod communities (Molina-Montenegro et al., 2006; Molenda et al., 2012). For instance, by maintaining their effect on temperature and nutrients, the positive effect of cushions on neighboring plants is accentuated by environmental stress (Arroyo et al., 2003; Badano and Cavieres, 2006; Antonsson et al., 2009; Yang et al., 2010; Anthelme et al., 2012). One can assume that cushion plants should similarly structure the composition of microbial communities within cliff soils along environmental gradients. Inside the cushion, we predict a convergence of microbial communities due to the local environmental buffering that is created by the cushion plant. Outside the cushion, we anticipate contrasting communities due to their response to bedrock type and elevation.

The goal of this study was to determine the extent to which cushions affect the abiotic characteristics of the surrounding soils and the associated bacterial and fungal communities along the elevation gradient and on different bedrock types. We chose Silene acaulis (Caryophyllaceae) as our study species. This alpine species is common in fell-fields and cliff ecosystems. It forms large cushions (up to 60 cm in diameter), occurs over a large elevation range (from nearly 2000 to 3000 masl) and is able to grow on both calcareous and siliceous bedrocks. We collected soil from inside and outside of S. acaulis cushions on highly rocky slopes and cliffs, along replicated elevational transects in two mountains ranges that differed in bedrock type.

Cushion plants affect the composition of both bacterial and fungal communities weakly but significantly, despite variability in both In and Out communities (Table 1; Figure 4). This relationship was observed regardless of the strategy that was adopted in the permutation procedure that was used for variance partitioning. This result emphasizes the multiple-scale effect of cushion plants on microbial community composition, from the population level to the scale of the whole study, which spans two mountain ranges with distinct bedrock types. Interestingly, we observed contrasting responses of the bacterial and fungal communities to the biotic and abiotic environments.

The bacterial communities in Out habitat were predominantly affected by bedrock type and, to a lesser extent, elevation. By contrast, beta-diversity in In habitat was strongly reduced, indicating a convergence of the communities under the cushions on both calcareous and siliceous bedrock and at both high and low elevation. Furthermore, the In-Out bacterial beta-diversity was correlated with pH. Soil pH was thus the best and main variable for explaining the patterns of bacterial beta-diversity among In and Out habitats. We also identified a response to elevation that may be linked to the shift in the nutrient content (Table 1; Figure 3; Table A1 in Appendix) because the shift in community composition occurred on siliceous bedrock only. The strong bedrock effect on community composition led to the selection of different bacterial communities according to the bedrock (Table 1). Soil pH is a well-known key factor influencing bacterial richness and community composition (Fierer and Jackson, 2006; Hogberg et al., 2007; Zinger et al., 2011; Shahnavaz et al., 2012). On average, the soil pH varied by ∼3.5 U (from 3.5 to 8.5) among bedrock types (Figure 2) but only ∼1 U (from 6 to 8.5) among cushions that were established on calcareous and siliceous bedrock types due to an increase in the soil pH inside the cushions that were located on siliceous bedrock (Figure 2). Lauber et al. (2009) observed that the effect of pH was particularly strong in acidic conditions and, more generally, when soil pH ranged between 4 and 6, leveling off above pH 6. Our experiment was not designed to identify the source of In communities, and more information about the species distributions or dispersal would be necessary to determine their sources. However the reduction of bacterial beta-diversity, together with the similarity of certain Out and In communities that was observed in PCoA ordination (Figure 4A) and the relatively weak values of the In-Out beta-diversity (Figure 5A), suggests that bacterial communities in In habitats are likely a subset of the bacterial communities in Out habitats. Such a feature is consistent with earlier reports suggesting that the soil surrounding plants seems to constitute the main source of rhizospheric microbial communities (Berg and Smalla, 2009). By providing a more homogeneous habitat with consistently enhanced C, N, N - NH4+, and SWC content and buffered soil pH, the cushions of S. acaulis act as a biotic filter on bacterial beta-diversity that counteracts the influence of the local environmental context, particularly bedrock type, likely recruiting and/or excluding bacterial taxa that contribute to the outside cushion community variability.

The patterns of the fungal communities were less obvious and much more variable than those of the bacterial communities. The fungal communities from In habitats were as variable as those from Out habitats (Figure 4B; Table 1), with several differences. The differences between Out communities were mainly but weakly related to soil pH, reflecting differences in community compositions between bedrock types (Figure 4B). By contrast, differences between In communities correlated with soil C, N - NH4+, and SWC, reflecting differences between cushions established on calcareous or siliceous bedrocks and at low or high elevation (Figure 4B; Table 1). The weak effect of soil pH on fungal communities compared to that observed for bacteria has already been reported in both arable (Rousk et al., 2010) and alpine grasslands soils (Zinger et al., 2011). These studies further reveal that fungal beta-diversity is instead related to soil nutrient status, and our results confirmed this trend. The effect of pH in Out habitats is overwhelmed in In habitats by the response of fungi to nutrient content. The absence of plants in Out habitat, together with nutrient limitations and the combined disturbance of oscillating climatic extremes and soil movement typical in alpine soils (Körner, 2003), could preclude the growth and hamper the hyphal proliferation of many fungi due to their typical mycorrhizal or saprophytic status, which is supported by the difficulties we encountered in amplifying fungal DNA from these samples. Thus, we hypothesize that by providing a nutritional resource and stable substrate, cushions sustain the growth of many more fungi than do open areas. In this sense, a study in the Andean alpine ecosystem reported that cushions of A. madreporica contain more spores of AM fungi than retrieved on open areas (Casanova-Katny et al., 2011). Overall, there is a strong link between the soil nutritive status of cushions, the environmental context in which they established and the associated fungal communities. Furthermore, cushions counteracted the effect of pH on the fungal community composition. As observed for bacteria, fungal beta-diversity patterns in In habitats differed from the ones in Out habitats.

The higher variability observed in fungal patterns compared to bacteria and the low variability that we were able to explain could be due to several factors. We followed different molecular markers; the V3 region of the 16S rRNA gene (bacterial marker) is most likely more phylogenetically conserved than the ITS1 region (fungal marker) (Brown et al., 2005). Other studies using the same or other molecular markers have also reported that fungal community patterns are difficult to interpret, yielding minimally explanatory models (Costa et al., 2006; Mougel et al., 2006; Hovatter et al., 2011; Zinger et al., 2011), which may be due to the patchy distribution of soil fungi (Manter et al., 2010). The response of bacteria and fungi to abiotic variables was still significant after controlling for geographic distance, which supports the link between microbial community composition and its response to environmental gradients, but key environmental variables or the appropriate spatial scale may also not have been considered for fungi.

Finally, the magnitude of the change in the microbial community composition between In and Out habitats (In-Out beta-diversity) varied along environmental gradients (Figure 5). The In-Out bacterial beta-diversity was correlated with the modification of soil pH and was, therefore, higher on siliceous bedrock (Figure 5A; Table A2 in Appendix). Moreover, bacterial communities responded to elevation solely in Out habitat on siliceous bedrock, supporting a strong cushion effect on siliceous bedrock. Because the fungi responded more strongly to soil nutrients, the In-Out fungal beta-diversity was higher on siliceous bedrock and at high elevations (Figure 5B; Table A2 in Appendix). On siliceous bedrock and at high elevations, conditions in Out habitat were more acidic (siliceous bedrock) and nutrient-limited (siliceous bedrock and at high elevation). Interestingly, the cushions located in these constrained conditions were richer in nutrients than cushions located in less constrained conditions, and strongly modified the soil pH (Figures 2 and 3), resulting in significant and even stronger ecosystem engineering. Although the In-Out fungal beta-diversity did not correlate with the respective abiotic modifications, it was generally higher at sites where the abiotic modification was higher. The fact that we did not observe pair-wise relationships may be because different factors structured the fungal communities in In and Out habitats. Thus, our observations indicate that the link between microbes and abiotic modification depends on the intensity of the abiotic stress mitigated by engineering organisms, as concluded in earlier works (Wright et al., 2006; Navel et al., 2012), but we suggest that a plant factor could be involved, either directly (via intraspecific variability) or indirectly (via physiological response to environmental harshness). Overall, these results suggest that the selective effect of cushions on bacterial and fungal communities could be particularly strong under more extreme conditions.

There is a growing body of evidence suggesting that cushion plants represent benefactor species or “nurse plants” that facilitate the recruitment of other plants (Arroyo et al., 2003; Cavieres et al., 2006; Antonsson et al., 2009) and arthropods (Molina-Montenegro et al., 2006; Molenda et al., 2012). Several studies have reported that the magnitude of facilitation by cushion plants, including S. acaulis, increases with environmental stress in alpine and arctic biomes on several mountains worldwide (Arroyo et al., 2003; Cavieres et al., 2006; Antonsson et al., 2009; Yang et al., 2010; Anthelme et al., 2012). These studies note that the local amelioration of climatic variables (e.g., temperatures) is involved (Arroyo et al., 2003; Cavieres et al., 2007), although nutrient enrichment is also a factor (Yang et al., 2010; Anthelme et al., 2012) and is more pronounced under stressful conditions, as observed here for nutrients, water and microbial communities. Our study opens a new avenue to understanding the ecology of these nurse plants from a microbial perspective. Several studies have reported that microbes act as the third party in plant–plant interactions (Callaway et al., 2007). Further work is needed to establish the linkages between plant–microbe interactions and plant–plant interactions in this particular model. For instance, it has been demonstrated that native plant species growing inside cushions in Andean alpine environments display enhanced AM mycorrhizal status compared to those growing outside (Casanova-Katny et al., 2011). Different functional groups of microbes can have different roles in the functioning of the cushion system or different links with the plant species that grow inside cushions. In this study, we demonstrated that bacteria and fungi differed in their relationships to the modification of soil abiotic properties by cushions. Additional studies are needed to disentangle the influence of microbial communities on the recruitment of taxa at higher trophic levels as well as how that recruitment influences the microbial communities that are associated with cushions. Plants growing inside cushions could influence the composition of soil microbes and their response to environmental gradients through mycorrhizal interactions or by providing new sources of organic matter.

It is possible that the cushion effect that was observed here could be applicable to other non-cushion-forming alpine plants because of possible similar abiotic modifications via organic matter deposition. Nevertheless, our results support the view that S. acaulis is a foundation species in the alpine ecosystem (Molenda et al., 2012) because of its effect on the structure of many trophic levels (Antonsson et al., 2009; Molenda et al., 2012). Overall, cushions constitute a unique habitat in extreme cliff ecosystems with modified local habitat conditions. Their presence significantly affects the beta-diversity patterns of bacterial and fungal communities. The bacterial and fungal communities do not respond similarly to the presence of cushions, likely because they are not sensitive to the same set of abiotic soil parameters. For both communities, the plants induce different responses to bedrock and elevation compared to the outside, but the response was inverse between bacteria and fungi; while plants had a buffering effect on bacterial communities, they exacerbated the response of fungi to bedrock and elevation. Our results support that habitat type differentially influences the distribution of soil microbes (Fierer et al., 2011; Hovatter et al., 2011) and that their response to environmental gradients depends on the taxa and microbial domain investigated (Singh et al., 2012; Wang et al., 2012). We demonstrated that there might be fundamental differences in the mechanisms underlying these molecular diversity patterns. Dissimilarities in the bacterial and fungal community between In and Out habitats were both positively related to the magnitude of habitat modification (i.e., higher in harsher conditions). Our results stress the need for integrated studies of the nurse effect of alpine cushions in which great attention should be paid to the role of microorganisms and their distribution in determining the outcome of plant–plant interactions and the biogeochemical functioning of these islands of fertility.

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.