Unraveling phase-dependent variations of viral community, virus-host linkage, and functional potential during manure composting process

IF 9 1区环境科学与生态学 Q1 AGRICULTURAL ENGINEERING Bioresource Technology Pub Date : 2025-01-16 DOI:10.1016/j.biortech.2025.132081

Zhengyuan Zhou , Songfeng Liu , Muhammad Saleem , Fei Liu , Ruiwen Hu , Hualong Su , Da Dong , Zhiwen Luo , Yongjie Wu , Yan Zhang , Zhili He , Cheng Wang

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Abstract

The temporal dynamics of bacterial and fungal communities significantly impact the manure composting process, yet viral communities are often underexplored. Bulk metagenomes, viromes, metatranscriptomes, and metabolomes were integrated to investigate dynamics of double-stranded DNA (dsDNA) virus and virus-host interactions throughout a 63-day composting process. A total of 473 viral operational taxonomic units (vOTUs), predominantly Caudoviricetes, showed distinct phase-dependent differentiation. In phase I (initial-mesophilic), viruses targeted Gammaproteobacteria and Firmicutes, utilizing restriction-modification (RM) systems. In phase II (thermophilic-maturing), viruses infected Alphaproteobacteria, Chloroflexi, and Planctomycetes, employing CRISPR-Cas systems. Lysogenic and lytic viruses exerting differential effects on bacterial pathogens across phases. Additionally, six types of auxiliary metabolic genes (AMGs) related to galactose and cysteine metabolisms were identified. The homologous lineages of AMGs with bacterial genes, along with the significant temporal correlation observed between virus-host-metabolite interactions, underscore the critical yet often overlooked role of viral communities in modulating microbial metabolisms and pathogenesis within composting ecosystems.

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揭示粪便堆肥过程中病毒群落、病毒-宿主连锁和功能潜力的阶段依赖性变化。

细菌和真菌群落的时间动态显著影响粪肥堆肥过程，但病毒群落往往未被充分探索。整合了大量宏基因组、病毒组、亚转录组和代谢组，以研究在63天的堆肥过程中双链DNA （dsDNA）病毒和病毒-宿主相互作用的动力学。473个病毒操作分类单位（vOTUs）表现出明显的相依赖分化，以尾状孢子为主。在第一阶段（初始-嗜中温），病毒利用限制性修饰（RM）系统靶向γ变形杆菌和厚壁菌门。在II期（嗜热成熟）中，利用CRISPR-Cas系统，病毒感染了甲变形菌、氯霉素和plantomycetes。溶原性和溶解性病毒在不同阶段对细菌病原体产生不同的影响。此外，还鉴定出6种与半乳糖和半胱氨酸代谢相关的辅助代谢基因（AMGs）。AMGs与细菌基因的同源谱系，以及在病毒-宿主-代谢物相互作用之间观察到的显著时间相关性，强调了病毒群落在调节堆肥生态系统中微生物代谢和发病机制方面的关键作用，但往往被忽视。

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来源期刊

Bioresource Technology 工程技术-能源与燃料

CiteScore

20.80

自引率

19.30%

发文量

2013

审稿时长

12 days

期刊介绍： Bioresource Technology publishes original articles, review articles, case studies, and short communications covering the fundamentals, applications, and management of bioresource technology. The journal seeks to advance and disseminate knowledge across various areas related to biomass, biological waste treatment, bioenergy, biotransformations, bioresource systems analysis, and associated conversion or production technologies. Topics include: • Biofuels: liquid and gaseous biofuels production, modeling and economics • Bioprocesses and bioproducts: biocatalysis and fermentations • Biomass and feedstocks utilization: bioconversion of agro-industrial residues • Environmental protection: biological waste treatment • Thermochemical conversion of biomass: combustion, pyrolysis, gasification, catalysis.