Conversion of the Amazon rainforest to agriculture results in biotic homogenization of soil bacterial communities

Abstract

The Amazon rainforest is the Earth's largest reservoir of plant and animal diversity, and it has been subjected to especially high rates of land use change, primarily to cattle pasture. This conversion has had a strongly negative effect on biological diversity, reducing the number of plant and animal species and homogenizing communities. We report here that microbial biodiversity also responds strongly to conversion of the Amazon rainforest, but in a manner different from plants and animals. Local taxonomic and phylogenetic diversity of soil bacteria increases after conversion, but communities become more similar across space. This homogenization is driven by the loss of forest soil bacteria with restricted ranges (endemics) and results in a net loss of diversity. This study shows homogenization of microbial communities in response to human activities. Given that soil microbes represent the majority of biodiversity in terrestrial ecosystems and are intimately involved in ecosystem functions, we argue that microbial biodiversity loss should be taken into account when assessing the impact of land use change in tropical forests.

Fig. 1.

Bacterial community composition of pasture and forest soil samples. (A) Distribution of 16S rRNA sequences across bacterial phyla in forest and pasture. (B) Nonmetric multidimensional scaling plot of taxonomic similarity (Bray–Curtis). (C) Nonmetric multidimensional scaling plot of phylogenetic similarity (FastUnifrac). Gray circles, pasture samples; black circles, forest samples.

Fig. 2.

Response of local diversity to ecosystem conversion. (A) Estimated taxonomic richness (abundance-based coverage estimator), (B) PD. Means (n = 33) are depicted, ±95% CI.

Fig. 3.

Response of community similarity to ecosystem conversion. (A) Average taxonomic similarity (Bray–Curtis), (B) Average phylogenetic similarity (FastUnifrac). Means (n = 435) are depicted, ±95% CI.

Fig. 4.

Response of community turnover to ecosystem conversion. (A) Decay of taxonomic similarity (Bray–Curtis) with geographic distance in forest. (B) Decay of taxonomic similarity (Bray–Curtis) with geographic distance in pasture. (C) Decay of phylogenetic similarity (FastUnifrac) with geographic distance in forest. (D) Decay of phylogenetic similarity (FastUnifrac) with geographic distance in pasture.

Fig. 5.

Distribution of bacterial OTUs across soil cores. (A) Distribution in forest and pasture of OTUs shared between forest and pasture. (B) Distribution in forest of OTUs unique to forest and OTUs shared between forest and pasture.