The consequences of deforestation and agricultural treatments are complex and affect all trophic levels. Changes of microbial community structure and composition associated with rainforest conversion to managed systems such as rubber and oil palm plantations have been shown by 16S rRNA gene analysis previously, but functional profile shifts have been rarely addressed. In this study, we analysed the effects of rainforest conversion to different converted land use systems, including agroforestry (“jungle rubber”) and monoculture plantations comprising rubber and oil palm, on soilborne microbial communities by metagenomic shotgun sequencing in Sumatra, Indonesia. The diversity of bacteria and archaea decreased whereas diversity of fungi increased in the converted land use systems. The soil microbiome was dominated by bacteria followed by fungi. We detected negative effects of land use conversion on the abundance of Proteobacteria (especially on Rhizobiales and Burkholderiales) and positive effects on the abundance of Acidobacteria and Actinobacteria. These abundance changes were mainly driven by pH, C:N ratio, and Fe, C and N content. With increasing land use intensity, the functional diversity decreased for bacteria, archaea and fungi. Gene abundances of specific metabolisms such as nitrogen metabolism and carbon fixation were affected by land use management practices. The abundance of genes related to denitrification and nitrogen fixation increased in plantations while abundance of genes involved in nitrification and methane oxidation showed no significant difference. Linking taxonomic and functional assignment per read indicated that nitrogen metabolism-related genes were mostly assigned to members of the Rhizobiales and Burkholderiales. Abundances of carbon fixation genes increased also with increasing land use intensity. Motility- and interaction-related genes, especially genes involved in flagellar assembly and chemotaxis genes, decreased towards managed land use systems. This indicated a shift in mobility and interspecific interactions in bacterial communities within these soils. Rainforest conversion to managed land use systems drastically affects structure and functional potential of soil microbial communities. The decrease in motility- and interaction-related functions from rainforest to converted land use systems indicated not only a shift in nutrient cycling but also in community dynamics. Fertilizer application and correspondingly higher availability of nutrients in intensively managed plantations lead to an environment in which interspecific interactions are not favoured compared to rainforest soils. We could directly link effects of land management, microbial community structure and functional potential for several metabolic processes. As our study is the first study of this size and detail on soil microbial communities in tropical systems, we provide a basis for further analyses.

中文翻译：

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揭示热带土地利用转化对土壤微生物组的影响

毁林和农业处理的后果是复杂的，并影响所有营养级别。先前已通过16S rRNA基因分析显示了与雨林转化为受管理系统（例如橡胶和油棕人工林）相关的微生物群落结构和组成的变化，但很少解决功能变化。在这项研究中，我们通过宏基因组shot弹枪测序分析了印度尼西亚苏门答腊岛上雨林转变为包括农用林业（“丛林橡胶”）和包括橡胶和油棕的单一种植人工林在内的不同转化土地利用系统对土壤微生物群落的影响。在转换后的土地利用系统中，细菌和古细菌的多样性减少，而真菌的多样性增加。土壤微生物组主要是细菌，其次是真菌。我们检测到土地利用转换对变形杆菌数量（尤其是对根瘤菌和伯克霍尔德里亚斯菌）的负面影响，以及对酸性细菌和放线菌数量的积极影响。这些丰度变化主要由pH，C：N比以及Fe，C和N含量驱动。随着土地利用强度的增加，细菌，古细菌和真菌的功能多样性下降。土地利用管理实践会影响特定代谢的基因丰度，例如氮代谢和固碳。人工林中与反硝化和固氮相关的基因丰富度增加，而与硝化和甲烷氧化有关的基因丰富度没有显着差异。将每次阅读的分类和功能分配联系起来，表明氮代谢相关基因主要分配给根瘤菌和伯克霍尔德氏菌的成员。固碳基因的丰度也随着土地利用强度的增加而增加。动力和相互作用相关的基因，特别是涉及鞭毛装配和趋化性基因的基因，在管理土地利用系统中下降了。这表明这些土壤中细菌群落的迁移率和种间相互作用发生了变化。将雨林转换为可管理的土地利用系统会极大地影响土壤微生物群落的结构和功能潜力。从热带雨林到土地利用转换系统，与运动和互动相关的功能减少，不仅表明养分循环发生变化，而且社区动态也发生了变化。在集约经营的人工林中，施肥和相应提高养分利用率导致了一种环境，在这种环境中，与雨林土壤相比，种间相互作用不利。我们可以直接将土地管理，微生物群落结构和功能潜力对几种代谢过程的影响联系起来。由于我们的研究是关于热带系统中土壤微生物群落大小和细节的首次研究，因此我们提供了进一步分析的基础。