Cook Ryan, Hooton Steve, Trivedi Urmi, King Liz, Dodd Christine E R, Hobman Jon L, Stekel Dov J, Jones Michael A, Millard Andrew D
School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK.
School of Biosciences, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK.
Microbiome. 2021 Mar 20;9(1):65. doi: 10.1186/s40168-021-01010-3.
Viruses are the most abundant biological entities on Earth, known to be crucial components of microbial ecosystems. However, there is little information on the viral community within agricultural waste. There are currently ~ 2.7 million dairy cattle in the UK producing 7-8% of their own bodyweight in manure daily, and 28 million tonnes annually. To avoid pollution of UK freshwaters, manure must be stored and spread in accordance with guidelines set by DEFRA. Manures are used as fertiliser, and widely spread over crop fields, yet little is known about their microbial composition. We analysed the virome of agricultural slurry over a 5-month period using short and long-read sequencing.
Hybrid sequencing uncovered more high-quality viral genomes than long or short-reads alone; yielding 7682 vOTUs, 174 of which were complete viral genomes. The slurry virome was highly diverse and dominated by lytic bacteriophage, the majority of which represent novel genera (~ 98%). Despite constant influx and efflux of slurry, the composition and diversity of the slurry virome was extremely stable over time, with 55% of vOTUs detected in all samples over a 5-month period. Functional annotation revealed a diverse and abundant range of auxiliary metabolic genes and novel features present in the community, including the agriculturally relevant virulence factor VapE, which was widely distributed across different phage genera that were predicted to infect several hosts. Furthermore, we identified an abundance of phage-encoded diversity-generating retroelements, which were previously thought to be rare on lytic viral genomes. Additionally, we identified a group of crAssphages, including lineages that were previously thought only to be found in the human gut.
The cattle slurry virome is complex, diverse and dominated by novel genera, many of which are not recovered using long or short-reads alone. Phages were found to encode a wide range of AMGs that are not constrained to particular groups or predicted hosts, including virulence determinants and putative ARGs. The application of agricultural slurry to land may therefore be a driver of bacterial virulence and antimicrobial resistance in the environment. Video abstract.
病毒是地球上数量最多的生物实体，是微生物生态系统的关键组成部分。然而，关于农业废弃物中的病毒群落信息却很少。英国目前约有270万头奶牛，每天产生的粪便量相当于其自身体重的7 - 8%，每年达2800万吨。为避免污染英国淡水，粪便必须按照环境、食品和农村事务部（DEFRA）制定的指南进行储存和撒施。粪便被用作肥料，广泛施用于农田，但对其微生物组成了解甚少。我们使用短读长和长读长测序技术，对农业粪肥5个月期间的病毒群落进行了分析。
混合测序比单独使用长读长或短读长发现了更多高质量的病毒基因组；共产生7682个病毒操作分类单元（vOTU），其中174个是完整的病毒基因组。粪肥病毒群落高度多样，以裂解性噬菌体为主，其中大多数代表新属（约98%）。尽管粪肥不断流入和流出，但随着时间推移，粪肥病毒群落的组成和多样性极其稳定，在5个月期间所有样本中检测到55%的vOTU。功能注释揭示了群落中存在的各种丰富的辅助代谢基因和新特征，包括与农业相关的毒力因子VapE，它广泛分布于不同的噬菌体属中，预计可感染多种宿主。此外，我们发现了大量噬菌体编码的多样性产生反转录元件，这些元件以前被认为在裂解性病毒基因组中很少见。此外，我们还鉴定出一组交叉噬菌体，包括以前认为只存在于人类肠道中的谱系。
牛粪肥病毒群落复杂、多样，以新属为主，其中许多仅使用长读长或短读长无法发现。发现噬菌体编码了广泛的辅助代谢基因，这些基因不限于特定群体或预测宿主，包括毒力决定因素和假定的抗生素抗性基因。因此，将农业粪肥施用于土地可能是环境中细菌毒力和抗菌素耐药性的驱动因素。视频摘要。
