Data from: The impact of tropical forest logging and oil palm agriculture on the soil microbiome

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.

选择性采伐与森林转化为油棕种植园正快速改变热带森林的原有面貌。目前学界对土壤微生物组（soil microbiome）响应这类土地利用变化的功能机制仍不甚明晰。本研究通过16S rRNA基因（16S rRNA gene）测序与鸟枪宏基因组（shotgun metagenomic）测序技术，对比了婆罗洲沙巴地区未采伐、单次采伐、两次采伐的热带雨林，以及转化为油棕种植园的区域的土壤生物群（soil biota）组成与功能属性。尽管采伐历史未对土壤群落产生显著影响，但研究发现原生林与采伐林的分类学及功能组成，与油棕种植园之间均存在显著差异。油棕种植园土壤中，与DNA、RNA、蛋白质代谢及其他核心代谢功能相关的基因丰度更高；反之，与次生代谢和细胞间互作相关的基因丰度更低，这表明在贫营养（oligotrophic）的油棕生境中，拮抗或共生作用的重要性大幅降低。总体而言，本研究结果显示，油棕种植园与森林的土壤微生物分类组成及功能基因多样性存在显著差异，但原生林与不同采伐历史的林分之间并无显著差异。这进一步佐证了采伐林仍保留原始土壤群落多数特征与功能的观点。不过，基于分类学与功能间强相关性构建的共现网络分析显示，采伐活动与油棕种植均会意外提升网络复杂度，表明两类土地利用变化对土壤微生物互作均存在广泛影响。