Virus impacted community adaptation in oligotrophic groundwater environment revealed by Hi-C coupled metagenomic and viromic study

Cheng，Zhanwen1,2; Li，Xiang1,2,3; Palomo，Alejandro1,2,3; Yang，Qing1,2; Han，Long1,2; Wu，Ziqi1,2; Li，Zengyi1,2; Zhang，Miao1,2; Chen，Liming1,2; Zhao，Bixi1,2; Yu，Kaiqiang1,2; Zhang，Chuanlun4,5; Hou，Shengwei4,5; Zheng，Yan1,2,3,4; Xia，Yu1,2,3

2023-09-15

10.1016/j.jhazmat.2023.131944

Journal of Hazardous Materials   Impact Factor & Quartile

0304-3894

1873-3336

Viruses play a crucial role in microbial mortality, diversity and biogeochemical cycles. Groundwater is the largest global freshwater and one of the most oligotrophic aquatic systems on Earth, but how microbial and viral communities are shaped in this special habitat is largely unexplored. In this study, we collected groundwater samples from 23 to 60 m aquifers at Yinchuan Plain, China. In total, 1920 non-reductant viral contigs were retrieved from metagenomes and viromes constructed by Illumina and Nanopore hybrid sequencing. Only 3% of them could be clustered with known viruses, most of which were Caudoviricetes. Coupling 1.2 Tb Hi-C sequencing with CRISPR matching and homology search, we connected 469 viruses with their hosts while some viral clusters presented a broad-host-range trait. Meanwhile, a large proportion of biosynthesis related auxiliary metabolism genes were identified. Those characteristics might benefit viruses for a better survival in this special oligotrophic environment. Additionally, the groundwater virome showed genomic features distinct from those of the open ocean and wastewater treatment facilities in GC distribution and unannotated gene compositions. This paper expands the current knowledge of the global viromic records and serves as a foundation for a more thorough understanding of viruses in groundwater.

Auxiliary metabolism genes Groundwater virus Hi-C Nanopore sequencing Virome

SCI

English

First ; Corresponding

National Natural Science Foundation of China[41831279];National Natural Science Foundation of China[42107257];

Engineering ; Environmental Sciences & Ecology

Engineering, Environmental ; Environmental Sciences

WOS:001037024500001

ELSEVIER

ENGINEERING

2-s2.0-85163980005

Scopus

1.School of Environmental Science and Engineering,Southern University of Science and Technology,Shenzhen,518055,China
2.State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control,School of Environmental Science and Engineering,Southern University of Science and Technology,Shenzhen,518055,China
3.Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control,School of Environmental Science and Engineering,Southern University of Science and Technology,Shenzhen,518055,China
4.Shenzhen Key Laboratory of Marine Archaea Geo-Omics,Department of Ocean Science and Department of Ocean Science & Engineering,Southern University of Science and Technology,Shenzhen,518055,China
5.Southern Marine Science and Engineering Guangdong Laboratory,Guangzhou,510000,China

Cheng，Zhanwen,Li，Xiang,Palomo，Alejandro,et al. Virus impacted community adaptation in oligotrophic groundwater environment revealed by Hi-C coupled metagenomic and viromic study[J]. Journal of Hazardous Materials,2023,458.

Cheng，Zhanwen.,Li，Xiang.,Palomo，Alejandro.,Yang，Qing.,Han，Long.,...&Xia，Yu.(2023).Virus impacted community adaptation in oligotrophic groundwater environment revealed by Hi-C coupled metagenomic and viromic study.Journal of Hazardous Materials,458.

Cheng，Zhanwen,et al."Virus impacted community adaptation in oligotrophic groundwater environment revealed by Hi-C coupled metagenomic and viromic study".Journal of Hazardous Materials 458(2023).