Susi Hanna, Filloux Denis, Frilander Mikko J, Roumagnac Philippe, Laine Anna-Liisa
Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, University of Helsinki, Finland.
CIRAD, BGPI, Montpellier, France.
PeerJ. 2019 Jan 11;7:e6140. doi: 10.7717/peerj.6140. eCollection 2019.
Wild plant populations may harbour a myriad of unknown viruses. As the majority of research efforts have targeted economically important plant species, the diversity and prevalence of viruses in the wild has remained largely unknown. However, the recent shift towards metagenomics-based sequencing methodologies, especially those targeting small RNAs, is finally enabling virus discovery from wild hosts. Understanding this diversity of potentially pathogenic microbes in the wild can offer insights into the components of natural biodiversity that promotes long-term coexistence between hosts and parasites in nature, and help predict when and where risks of disease emergence are highest. Here, we used small RNA deep sequencing to identify viruses in populations, and to understand the variation in their prevalence and distribution across the Åland Islands, South-West Finland. By subsequent design of PCR primers, we screened the five most common viruses from two sets of plants: 164 plants collected from 12 populations irrespective of symptoms, and 90 plants collected from five populations showing conspicuous viral symptoms. In addition to the previously reported species (PlLV), we found four potentially novel virus species belonging to and genera. Our results show that virus prevalence and diversity varied among the sampled host populations. In six of the virus infected populations only a single virus species was detected, while five of the populations supported between two to five of the studied virus species. In 20% of the infected plants, viruses occurred as coinfections. When the relationship between conspicuous viral symptoms and virus infection was investigated, we found that plants showing symptoms were usually infected (84%), but virus infections were also detected from asymptomatic plants (44%). Jointly, these results reveal a diverse virus community with newly developed tools and protocols that offer exciting opportunities for future studies on the eco-evolutionary dynamics of viruses infecting plants in the wild.
野生植物种群可能蕴藏着无数未知病毒。由于大多数研究工作都针对具有经济重要性的植物物种，野生环境中病毒的多样性和流行情况在很大程度上仍不为人知。然而，最近向基于宏基因组学的测序方法的转变，尤其是针对小RNA的方法，最终使得从野生宿主中发现病毒成为可能。了解野生环境中这种潜在致病微生物的多样性，有助于深入了解促进宿主与寄生虫在自然界长期共存的自然生物多样性组成部分，并有助于预测疾病出现风险最高的时间和地点。在这里，我们使用小RNA深度测序来鉴定种群中的病毒，并了解它们在芬兰西南部奥兰群岛的流行情况和分布变化。通过随后设计PCR引物，我们从两组植物中筛选出了五种最常见的病毒：从12个种群中采集的164株植物，不论有无症状；以及从五个出现明显病毒症状的种群中采集的90株植物。除了先前报道的物种（PlLV）外，我们还发现了四种可能属于和属的新型病毒物种。我们的结果表明，病毒的流行率和多样性在采样的宿主种群中各不相同。在六个受病毒感染的种群中，仅检测到一种病毒物种，而五个种群中存在两到五种所研究的病毒物种。在20%的受感染植物中，病毒以混合感染的形式出现。当研究明显的病毒症状与病毒感染之间的关系时，我们发现出现症状的植物通常受到感染（84%），但无症状植物中也检测到了病毒感染（44%）。综合来看，这些结果揭示了一个多样化的病毒群落，新开发的工具和方案为未来研究野生环境中感染植物的病毒的生态进化动态提供了令人兴奋的机会。
