Fungal palaeodiversity revealed using high-throughput metabarcoding of ancient DNA from arctic permafrost
Fungal palaeodiversity revealed using high-throughput metabarcoding of ancient DNA from arctic permafrost
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DOI：
10.1111/1462-2920.12020
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发表时间：
2013-04-01
影响因子：
5.1
通讯作者：
Brochmann, Christian
中科院分区：
文献类型：
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作者：
Bellemain, Eva;Davey, Marie L.;Brochmann, Christian
通过对冻土带保存的DNA进行下一代测序和元条形码分析，评估了古真菌群落的分类和生态多样性。研究人员对西伯利亚两个地区的26个沉积物样本进行了真菌ITS分析，这些样本的放射性碳年龄为1600032000年。我们检测到来自3门21目的75个真菌otu，尽管稀疏分析表明，尽管每个样本平均产生6677个+/- 3811个（平均+/- SD）序列，但未恢复全部多样性，并且保存偏差可能对恢复的DNA有相当大的影响。大多数otu（75.4%）代表子囊菌。由于测序深度不足、DNA降解和我们样本中可能存在的保存偏差，恢复的分类群可能不能代表完整的历史真菌群落，并且难以确定真菌群落是否在地理上发生了变化或在1600032000bp期间经历了组成变化。然而，对功能生态群的otu注释提供了丰富的历史群落信息。大约三分之一的otu被认为是植物伴生菌（病原体、腐养菌和内生菌），典型的禾本科和牧草丰富的栖息地。我们还检测到可能与古代昆虫和食草动物有关的昆虫病原体、嗜虫菌和亲角蛋白菌。假定的昆虫病原体、分枝寄生虫、水生真菌和内生菌的检测拓宽了我们以前对白令陆桥古生态系统中真菌多样性的认识。还发现了一大群假定的嗜冷/耐冷真菌，很可能代表了一个现代的、代谢活跃的真菌群落。
The taxonomic and ecological diversity of ancient fungal communities was assessed by combining next generation sequencing and metabarcoding of DNA preserved in permafrost. Twenty-six sediment samples dated 1600032000 radiocarbon years old from two localities in Siberia were analysed for fungal ITS. We detected 75 fungal OTUs from 21 orders representing three phyla, although rarefaction analyses suggested that the full diversity was not recovered despite generating an average of 6677 +/- 3811 (mean +/- SD) sequences per sample and that preservation bias likely has considerable effect on the recovered DNA. Most OTUs (75.4%) represented ascomycetes. Due to insufficient sequencing depth, DNA degradation and putative preservation biases in our samples, the recovered taxa probably do not represent the complete historic fungal community, and it is difficult to determine whether the fungal communities varied geographically or experienced a composition shift within the period of 1600032000 bp. However, annotation of OTUs to functional ecological groups provided a wealth of information on the historic communities. About one-third of the OTUs are presumed plant-associates (pathogens, saprotrophs and endophytes) typical of graminoid- and forb-rich habitats. We also detected putative insect pathogens, coprophiles and keratinophiles likely associated with ancient insect and herbivore faunas. The detection of putative insect pathogens, mycoparasites, aquatic fungi and endophytes broadens our previous knowledge of the diversity of fungi present in Beringian palaeoecosystems. A large group of putatively psychrophilic/psychrotolerant fungi was also detected, most likely representing a modern, metabolically active fungal community.