Advances in DNA extraction and next‐generation sequencing have made a vast number of historical herbarium specimens available for genomic investigation. These specimens contain not only genomic information from the individual plants themselves, but also from associated microorganisms such as bacteria and fungi. These microorganisms may have colonized the living plant (e.g., pathogens or host‐associated commensal taxa) or may result from postmortem colonization that may include decomposition processes or contamination during sample handling. Here we characterize the metagenomic profile from shotgun sequencing data from herbarium specimens of two widespread plant species (Ambrosia artemisiifolia and Arabidopsis thaliana) collected up to 180 years ago. We used blast searching in combination with megan and were able to infer the metagenomic community even from the oldest herbarium sample. Through comparison with contemporary plant collections, we identify three microbial species that are nearly exclusive to herbarium specimens, including the fungus Alternaria alternata, which can comprise up to 7% of the total sequencing reads. This species probably colonizes the herbarium specimens during preparation for mounting or during storage. By removing the probable contaminating taxa, we observe a temporal shift in the metagenomic composition of the invasive weed Am. artemisiifolia. Our findings demonstrate that it is generally possible to use herbarium specimens for metagenomic analyses, but that the results should be treated with caution, as some of the identified species may be herbarium contaminants rather than representing the natural metagenomic community of the host plant.

中文翻译：

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历史植物标本的宏基因组分析揭示了死后微生物群落。

DNA 提取和下一代测序的进步使大量历史标本馆标本可用于基因组研究。这些标本不仅包含来自单个植物本身的基因组信息，还包含来自相关微生物（如细菌和真菌）的基因组信息。这些微生物可能已经定植于活植物（例如，病原体或宿主相关的共生类群），或者可能来自死后定植，其中可能包括样品处理过程中的分解过程或污染。在这里，我们从两种广泛分布的植物物种（Ambrosia artemisiifolia和拟南芥）的标本馆标本的鸟枪法测序数据中表征宏基因组图谱。) 收集到 180 年前。我们将爆炸搜索与megan结合使用，甚至能够从最古老的植物标本馆样本中推断出宏基因组群落。通过与当代植物收藏的比较，我们确定了三种几乎不属于植物标本馆标本的微生物物种，包括真菌Alternaria alternata，其可占总测序读数的 7%。该物种可能在准备安装或储存期间定植于标本馆标本。通过去除可能的污染类群，我们观察到侵入性杂草Am的宏基因组组成的时间变化。青蒿. 我们的研究结果表明，通常可以使用植物标本进行宏基因组分析，但应谨慎对待结果，因为某些已鉴定物种可能是植物标本中的污染物，而不是代表宿主植物的天然宏基因组群落。