title: The impact of tropical forest logging and oil palm agriculture on the soil microbiome.
abstract: Selective logging and forest conversion to oil palm agriculture are rapidly altering tropical forests. However, functional responses of the soil microbiome to these land-use changes are poorly understood. Using 16S rRNA gene and shotgun metagenomic sequencing, we compared composition and functional attributes of soil biota between unlogged, once-logged and twice-logged rainforest, and areas converted to oil palm plantations in Sabah, Borneo. Although there was no significant effect of logging history, we found a significant difference between the taxonomic and functional composition of both primary and logged forests and oil palm. Oil palm had greater abundances of genes associated with DNA, RNA, protein metabolism and other core metabolic functions, but conversely, lower abundance of genes associated with secondary metabolism and cell-cell interactions, indicating less importance of antagonism or mutualism in the more oligotrophic oil palm environment. Overall, these results show a striking difference in taxonomic composition and functional gene diversity of soil microorganisms between oil palm and forest, but no significant difference between primary forest and forest areas with differing logging history. This reinforces the view that logged forest retains most features and functions of the original soil community. However, networks based on strong correlations between taxonomy and functions showed that network complexity is unexpectedly increased due to both logging and oil palm agriculture, which suggests a pervasive effect of both land-use changes on the interaction of soil microbes.
authors.affiliation: Department of Biological Science, College of Natural Sciences, Seoul National University, Seoul, 151-742, Korea.|Arctic Research Center, Korea Polar Research Institute, Incheon, 406-840, Korea.
authors.forename: Binu M
authors.initials: BM
authors.lastname: Tripathi
authors.affiliation: Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK.
authors.forename: David P
authors.initials: DP
authors.lastname: Edwards
authors.affiliation: Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo - USP. Av. Centenário, 303, CEP 13400-970 Piracicaba (SP), Brazil.|Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen 6708 PB, The Netherlands.
authors.forename: Lucas William
authors.initials: LW
authors.lastname: Mendes
authors.affiliation: Arctic Research Center, Korea Polar Research Institute, Incheon, 406-840, Korea.
authors.forename: Mincheol
authors.initials: M
authors.lastname: Kim
authors.affiliation: Department of Biological Science, College of Natural Sciences, Seoul National University, Seoul, 151-742, Korea.
authors.forename: Ke
authors.initials: K
authors.lastname: Dong
authors.affiliation: Celemics Inc., 19F, Bldg. A, BYC High city, 131, Gasandigital 1-ro, Geumcheon-gu, Seoul, 153-718, Korea.
authors.forename: Hyoki
authors.initials: H
authors.lastname: Kim
authors.affiliation: Department of Biological Science, College of Natural Sciences, Seoul National University, Seoul, 151-742, Korea.
authors.forename: Jonathan M
authors.initials: JM
authors.lastname: Adams
mesh_terms: D000383:Agriculture; D028023:Arecaceae / Q000254:growth & development; D001419:Bacteria / Q000145:classification; D044822:Biodiversity; D001893:Borneo; D003247:Conservation of Natural Resources; D016468:Forestry; D065928:Forests; D054892:Metagenome; D064307:Microbiota; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012988:Soil Microbiology
chemical_list: D012336:RNA, Ribosomal, 16S
keywords: functional diversity; oil palm plantation; selective logging; shotgun metagenomics; soil microbiome; tropical rainforest