Banchi Elisa, Stankovic David, Fernández-Mendoza Fernando, Gionechetti Fabrizia, Pallavicini Alberto, Muggia Lucia
1Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy.
2National Institute of Biology, Marine Biology Station, Fornače 41, 6330 Piran, Slovenia.
Mycol Prog. 2018;17(9):1049-1066. doi: 10.1007/s11557-018-1415-4. Epub 2018 Jun 22.
Lichen thalli harbor complex fungal communities (mycobiomes) of species with divergent trophic and ecological strategies. The complexity and diversity of lichen mycobiomes are still largely unknown, despite surveys combining culture-based methods and high-throughput sequencing (HTS). The results of such surveys are strongly influenced by the barcode locus chosen, its sensitivity in discriminating taxa, and the depth to which public sequence repositories cover the phylogenetic spectrum of fungi. Here, we use HTS of the internal transcribed spacer 2 (ITS2) to assess the taxonomic composition and diversity of a well-characterized, alpine rock lichen community that includes thalli symptomatically infected by lichenicolous fungi as well as asymptomatic thalli. Taxa belonging to the order Chaetothyriales are the major components of the observed lichen mycobiomes. We predict sequences representative of lichenicolous fungi characterized morphologically and assess their asymptomatic presence in lichen thalli. We demonstrated the limitations of metabarcoding in fungi and show how the estimation of species diversity widely differs when ITS1 or ITS2 are used as barcode, and particularly biases the detection of Basidiomycota. The complementary analysis of both ITS1 and ITS2 loci is therefore required to reliably estimate the diversity of lichen mycobiomes.
地衣叶状体中存在着复杂的真菌群落（真菌微生物组），这些真菌物种具有不同的营养和生态策略。尽管有基于培养的方法和高通量测序（HTS）相结合的调查，但地衣真菌微生物组的复杂性和多样性仍很大程度上未知。此类调查的结果受到所选条形码基因座、其区分分类群的敏感性以及公共序列库覆盖真菌系统发育谱深度的强烈影响。在这里，我们使用内部转录间隔区2（ITS2）的高通量测序来评估一个特征明确的高山岩石地衣群落的分类组成和多样性，该群落包括有地衣寄生真菌症状感染的叶状体以及无症状叶状体。属于座囊菌目的分类群是观察到的地衣真菌微生物组的主要组成部分。我们预测代表形态特征明确的地衣寄生真菌的序列，并评估它们在地衣叶状体中的无症状存在情况。我们展示了真菌代谢条形码分析的局限性，并表明当地衣ITS1或ITS2用作条形码时，物种多样性的估计差异很大，特别是对担子菌门的检测存在偏差。因此，需要对ITS1和ITS2基因座进行互补分析，以可靠地估计地衣真菌微生物组的多样性。
