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油棕种植业正快速改变热带森林。然而，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响应机制仍缺乏深入认知。本研究采用16S rRNA基因（16S rRNA gene）测序与鸟枪宏基因组测序（shotgun metagenomic sequencing）技术，对比了婆罗洲沙巴地区未采伐、一次采伐、两次采伐的雨林，以及转换为油棕种植园的样地中土壤生物群落的组成与功能属性。尽管采伐历史未对土壤生物群落产生显著影响，但我们发现原生林与各采伐林的分类学组成及功能组成，均与油棕样地存在显著差异。油棕样地中与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，但与之相反，与次生代谢及细胞间互作相关的基因丰度更低，这表明在寡营养程度更高的油棕生境中，拮抗作用与互利共生的重要性显著降低。总体而言，本研究结果显示，油棕样地与森林样地的土壤微生物分类学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地表征无显著差异。这进一步印证了采伐林仍保留原始土壤群落多数特征与功能的学术观点。然而，基于分类学与功能间强相关性构建的微生物互作网络分析显示，采伐与油棕种植活动均会意外提升网络复杂度，这表明两类土地利用变化均对土壤微生物的互作过程产生了广泛影响。