Denison Elizabeth R, Pound Helena L, Gann Eric R, Gilbert Naomi E, Weston David J, Pelletier Dale A, Wilhelm Steven W
Department of Microbiology, University of Tennessee, Knoxville, TN, USA.
Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
Environ Microbiome. 2025 Jun 5;20(1):62. doi: 10.1186/s40793-025-00719-0.
Viruses are an understudied component of plant microbiomes. Identifying viruses that are shared between individual plants, or members of the “core virome”, could reveal stable viral populations with the potential to modulate the composition and function of the microbiome. Here, we examined the virome associated with mosses, a keystone species that has direct influence over the fate of peatland carbon stores. We analyzed bulk metagenomes and metatranscriptomes generated from field samples collected over a ten-month period to identify virus-like sequences shared among plants.
Individual samples harbored distinct DNA and RNA viromes where only a small percentage (< 1%) of the total number of identified viral contigs were shared among all samples. Based on taxonomic classification, the shared viral contigs represent bacterial viruses, or phage (), as well as viruses of eukaryotes, namely nucleocytoplasmic large DNA viruses () and RNA viruses (). We linked the shared phage-like contigs to viral regions within sequenced genomes of bacterial taxa that are members of the core microbiome, suggesting that these contigs represent temperate phage or degraded prophage. The putative nucleocytoplasmic large DNA viruses and RNA viruses were phylogenetically diverse and showed sequence similarity to viruses associated with a broad range of hosts and environmental sources.
The identification of shared viral contigs suggested that, despite the compositional heterogeneity between samples, mosses may harbor a core virome. Future work validating the presence of the core virome is warranted as it may aid in understanding how persistent viruses impact microbiome ecology and symbiont evolution within this climatically relevant keystone species.
The online version contains supplementary material available at 10.1186/s40793-025-00719-0.
病毒是植物微生物组中研究较少的组成部分。识别个体植物之间共享的病毒，即“核心病毒组”的成员，可能会揭示出具有调节微生物组组成和功能潜力的稳定病毒群体。在这里，我们研究了与苔藓相关的病毒组，苔藓是一种对泥炭地碳储存命运有直接影响的关键物种。我们分析了在十个月期间收集的野外样本产生的宏基因组和宏转录组，以识别植物之间共享的病毒样序列。
单个样本含有不同的DNA和RNA病毒组，在所有样本中，仅一小部分（<1%）已识别的病毒重叠群是共享的。基于分类学分类，共享的病毒重叠群代表细菌病毒或噬菌体，以及真核生物病毒，即核质大DNA病毒和RNA病毒。我们将共享的噬菌体样重叠群与核心微生物组成员细菌类群的测序基因组中的病毒区域联系起来，表明这些重叠群代表温和噬菌体或降解的原噬菌体。推定的核质大DNA病毒和RNA病毒在系统发育上具有多样性，并且与与广泛宿主和环境来源相关的病毒显示出序列相似性。
共享病毒重叠群的识别表明，尽管样本之间存在组成异质性，但苔藓可能拥有核心病毒组。未来有必要开展工作验证核心病毒组的存在，因为这可能有助于理解持久性病毒如何影响这一与气候相关关键物种内的微生物组生态学和共生体进化。
在线版本包含可在10.1186/s40793-025-00719-0获取的补充材料。
