title: Soil microbiome responses to the short-term effects of Amazonian deforestation.
abstract: Slash-and-burn clearing of forest typically results in increase in soil nutrient availability. However, the impact of these nutrients on the soil microbiome is not known. Using next generation sequencing of 16S rRNA gene and shotgun metagenomic DNA, we compared the structure and the potential functions of bacterial community in forest soils to deforested soils in the Amazon region and related the differences to soil chemical factors. Deforestation decreased soil organic matter content and factors linked to soil acidity and raised soil pH, base saturation and exchangeable bases. Concomitant to expected changes in soil chemical factors, we observed an increase in the alpha diversity of the bacterial microbiota and relative abundances of putative copiotrophic bacteria such as Actinomycetales and a decrease in the relative abundances of bacterial taxa such as Chlamydiae, Planctomycetes and Verrucomicrobia in the deforested soils. We did not observe an increase in genes related to microbial nutrient metabolism in deforested soils. However, we did observe changes in community functions such as increases in DNA repair, protein processing, modification, degradation and folding functions, and these functions might reflect adaptation to changes in soil characteristics due to forest clear-cutting and burning. In addition, there were changes in the composition of the bacterial groups associated with metabolism-related functions. Co-occurrence microbial network analysis identified distinct phylogenetic patterns for forest and deforested soils and suggested relationships between Planctomycetes and aluminium content, and Actinobacteria and nitrogen sources in Amazon soils. The results support taxonomic and functional adaptations in the soil bacterial community following deforestation. We hypothesize that these microbial adaptations may serve as a buffer to drastic changes in soil fertility after slash-and-burning deforestation in the Amazon region.
authors: Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of São Paulo USP, Avenida Centenário 303, 13400-970, Piracicaba, SP, Brazil; Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.
authors: Acacio A
authors: AA
authors: Navarrete
authors: Siu M
authors: SM
authors: Tsai
authors: Lucas W
authors: LW
authors: Mendes
authors: Karoline
authors: K
authors: Faust
authors: Mattias
authors: M
authors: de Hollander
authors: Noriko A
authors: NA
authors: Cassman
authors: Jeroen
authors: J
authors: Raes
authors: Johannes A
authors: JA
authors: van Veen
authors: Eiko E
authors: EE
authors: Kuramae
mesh_terms: D000383:Agriculture / Q000379:methods; D001419:Bacteria / Q000145:classification*; D003247:Conservation of Natural Resources; D004269:DNA, Bacterial / Q000235:genetics; D065928:Forests; D059014:High-Throughput Nucleotide Sequencing; D064307:Microbiota; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012987:Soil / Q000737:chemistry; D012988:Soil Microbiology
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; D012987:Soil
keywords: 16S rRNA gene; bacterial networks; metagenomics; slash-and-burning; soil microbial ecology; tropical rainforest