Habitat fragmentation and soil biodiversity: Do soil microbes exhibit edge effects?

Background/Question/Methods

Preserving communities and ecosystem functioning in fragmented landscapes requires understanding how communities change near fragment edges. Such “edge effects” are driven by different abiotic and biotic conditions at edges and are widespread among animal and plant taxa. Limited, however, are studies on soil microorganisms. Microbes mediate soil fertility and nutrient cycling, but their small size means that their responses to edges may differ from those of larger organisms. To understand how soil microorganisms respond to habitat edges, we sampled and sequenced soil bacterial, archaeal, and fungal communities along transects spanning the edge between savanna patches and a forest matrix. We hypothesized that 1) more pronounced edge effects in community turnover would correlate with greater environmental contrast between adjacent habitats, 2) that edge effects would vary among taxa, and 3) that taxa with metabolically-diverse genomes or spore-forming genes would exhibit small edge responses. To investigate community-wide patterns, we explored how turnover across the transect related to vegetation and soil physicochemical characteristics. To understand edge effects and spillover of specific taxa, we fit logistic models to changes in abundance of each taxon across the edge, relating the observed patterns to genomic attributes.

Results/Conclusions

As hypothesized, soil microbiome turnover was correlated with the degree of contrast between the savanna and the forest. Specifically, differences among samples were explained by, in order of importance, contrast in canopy cover, place along the transect, pH, and vegetation cover. We also found that microbial taxa exhibited varied edge effects. About one third of sufficiently ubiquitous and abundant taxa changed in abundance at the edge but these varied widely in their edge sensitivity and penetration into the opposite habitat. Compared with taxa sensitive to the edge, taxa unaffected by the edge were more likely to have larger genomes and genes for spore-forming. These results suggest that the former group may be able to employ diverse metabolic strategies to live across the varied environmental conditions in our system, whereas the latter may be widespread because they can sporulate when in unfavorable conditions. Our work highlights that environmental variation and microbial traits can be used to predict edge effects in soil communities, which in turn may help conservation managers determine the size and condition of remnant habitat needed to maintain soil communities and healthy soils.