The health, growth, and fitness of boreal forest trees are impacted and improved by their associated microbiomes. Microbial gene expression and functional activity can be assayed with RNA sequencing (RNA-Seq) data from host samples. In contrast, phylogenetic marker gene amplicon sequencing data are used to assess taxonomic composition and community structure of the microbiome. Few studies have considered how much of this structural and taxonomic information is included in transcriptomic data from matched samples. Here, we described fungal communities using both host-derived RNA-Seq and fungal ITS1 DNA amplicon sequencing to compare the outcomes between the methods. We used a panel of root and needle samples from the coniferous tree species Picea abies (Norway spruce) growing in untreated (nutrient-deficient) and nutrient-enriched plots at the Flakaliden forest research site in boreal northern Sweden. We show that the relationship between samples and alpha and beta diversity indicated by the fungal transcriptome is in agreement with that generated by the ITS data, while also identifying a lack of taxonomic overlap due to limitations imposed by current database coverage. Furthermore, we demonstrate how metatranscriptomics data additionally provide biologically informative functional insights. At the community level, there were changes in starch and sucrose metabolism, biosynthesis of amino acids, and pentose and glucuronate interconversions, while processing of organic macromolecules, including aromatic and heterocyclic compounds, was enriched in transcripts assigned to the genus Cortinarius.

中文翻译：

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使用来自挪威云杉的元转录组学和内部转录间隔扩增子测序进行比较真菌群落分析

北方森林树木的健康、生长和健康受到其相关微生物组的影响和改善。微生物基因表达和功能活性可以通过来自宿主样本的 RNA 测序 (RNA-Seq) 数据进行分析。相比之下，系统发育标记基因扩增子测序数据用于评估微生物组的分类组成和群落结构。很少有研究考虑在匹配样本的转录组数据中包含多少这种结构和分类信息。在这里，我们使用宿主衍生的 RNA-Seq 和真菌 ITS1 DNA 扩增子测序描述了真菌群落，以比较两种方法之间的结果。我们使用了一组来自针叶树种Picea abies的根和针样本（挪威云杉）生长在瑞典北部 Flakaliden 森林研究地点的未经处理（营养缺乏）和营养丰富的地块中。我们表明，真菌转录组指示的样本与 alpha 和 beta 多样性之间的关系与 ITS 数据生成的结果一致，同时还确定由于当前数据库覆盖范围的限制而缺乏分类重叠。此外，我们展示了元转录组学数据如何额外提供生物学信息功能见解。在群落水平上，淀粉和蔗糖代谢、氨基酸的生物合成以及戊糖和葡萄糖醛酸的相互转化发生了变化，而有机大分子（包括芳香族和杂环化合物）的加工在分配给该属的转录本中得到了丰富科蒂纳留斯。