Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens.
Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens.
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DOI：
10.1186/s40168-021-01010-3
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发表时间：
2021-03-20
期刊：
影响因子：
15.5
通讯作者：
Millard AD
中科院分区：
文献类型：
--
作者：
Cook R;Hooton S;Trivedi U;King L;Dodd CER;Hobman JL;Stekel DJ;Jones MA;Millard AD
病毒是地球上数量最多的生物实体，是微生物生态系统的重要组成部分。然而，关于农业废弃物中病毒群落的信息很少。目前，英国约有270万头奶牛每天产生相当于自身体重7-8%的粪便，每年产生2800万吨粪便。为了避免污染英国的淡水，粪便必须按照DEFRA制定的指导方针储存和传播。粪肥被用作肥料，广泛地散布在农田里，但人们对它们的微生物组成知之甚少。我们使用短读和长读测序分析了5个月的农用浆液病毒组。混合测序比单独的长读或短读发现了更多高质量的病毒基因组；得到7682个votu，其中174个是完整的病毒基因组。浆液病毒体种类繁多，以裂解型噬菌体为主，绝大多数为新属（约98%）。尽管浆液不断流入和流出，但随着时间的推移，浆液病毒的组成和多样性非常稳定，在5个月的时间内，所有样品中检测到55%的votu。功能注释揭示了该群落中存在多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，该因子广泛分布于不同的噬菌体属，预计会感染几种宿主。此外，我们还发现了大量噬菌体编码的产生多样性的逆转录因子，这在以前被认为在裂解病毒基因组中很少见。此外，我们还发现了一组巨噬菌，包括以前认为只在人类肠道中发现的谱系。牛浆病毒体是复杂的，多样的，以新属为主，其中许多不能单独使用长或短读取恢复。研究发现噬菌体编码广泛的AMGs，这些AMGs不局限于特定的群体或预测的宿主，包括毒力决定因素和假定的ARGs。因此，农业泥浆在土地上的应用可能是环境中细菌毒力和抗菌素耐药性的驱动因素。视频摘要在线版本包含补充材料，可在10.1186/s40168-021-01010-3获得。
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 The online version contains supplementary material available at 10.1186/s40168-021-01010-3.
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DOI：
10.3390/v9040070
发表时间：
2017-04-03
期刊：
Viruses
影响因子：
--
作者：
Adriaenssens E;Brister JR
通讯作者：
Brister JR
影响因子：
15.5
作者：
Benler, Sean;Cobian-Gueemes, Ana Georgina;Rohwer, Forest
通讯作者：
Rohwer, Forest
影响因子：
28.3
作者：
Edwards, Robert A.;Vega, Alejandro A.;Dutilh, Bas E.
通讯作者：
Dutilh, Bas E.
影响因子：
2.3
作者：
Cook, Kimberly L.;Whitehead, Terence R.;Cotta, Michael A.
通讯作者：
Cotta, Michael A.
影响因子：
5.2
作者：
Castillo D;Pérez-Reytor D;Plaza N;Ramírez-Araya S;Blondel CJ;Corsini G;Bastías R;Loyola DE;Jaña V;Pavez L;García K
通讯作者：
García K