Species richness and phylogenetic diversity comparisons of soil microbial communities affected by nickel-mining and revegetation efforts in New Caledonia

Abstract

In order to understand the impact of human activities on soil microbial diversity, we investigated bacterial communities in samples recovered from four New Caledonia environments that have been disturbed by varying degrees of nickel mining associated activities: an undisturbed area with natural soil (characterized by pristine vegetation), a mine spoil (devoid of vegetation), two revegetated mine spoils by endemic plants. For each sample, total DNA was extracted and 16S rDNA clone library were constructed. 442 clones were sequenced and analyzed. Using these clones, diversity was estimated not only in terms of species richness (non-parametric estimators) and evenness (Reciprocal of Simpson's index), but also in terms of phylogenetic diversity (LIBSHUFF program). Statistically significant differences were detected in phylogenetic composition between mine spoils and natural soil ( p = 0.001), between revegetated soils and natural soil ( p = 0.001), and between revegetated soils and mine spoils ( p = 0.001). On the other hand, no significant differences in species richness were observed between the different environmental samples. These findings provide insights into the response of bacterial community following environmental perturbations caused by nickel-mining activities and revegetation efforts.