Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
Section for EvoGenomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Mol Ecol Resour. 2020 Sep;20(5):1206-1219. doi: 10.1111/1755-0998.13174. Epub 2020 May 18.
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.
DNA 提取和下一代测序技术的进步使得大量历史植物标本可用于基因组研究。这些标本不仅包含个体植物自身的基因组信息，还包含来自相关微生物（如细菌和真菌）的信息。这些微生物可能已经在活体植物上定殖（例如病原体或与宿主相关的共生类群），也可能是死后定殖的结果，包括分解过程或在样本处理过程中的污染。在这里，我们对来自两个广泛分布的植物物种（豚草和拟南芥）的植物标本的鸟枪法测序数据进行了宏基因组特征分析，这些标本采集于 180 年前。我们使用 blast 搜索结合 megan 来推断宏基因组群落，即使是最古老的植物标本也可以推断出其宏基因组群落。通过与当代植物收集物进行比较，我们确定了三种几乎只存在于植物标本中的微生物物种，包括占总测序reads 比例高达 7%的Alternaria alternata 真菌。该物种可能在植物标本准备装裱或储存期间定殖于植物标本上。通过去除可能的污染类群，我们观察到入侵杂草豚草的宏基因组组成发生了时间上的变化。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，但结果应谨慎处理，因为一些鉴定出的物种可能是植物标本的污染物，而不是宿主植物的自然宏基因组群落的代表。
