Diversity and ecological roles of hidden viral players in groundwater microbiomes

TL;DR

This study explores the role of viruses in groundwater ecosystems, revealing their impact on microbial communities and nutrient cycling.

Contribution

The study identifies a vast number of novel viral sequences and their potential roles in shaping groundwater microbial dynamics.

Findings

257,252 viral operational taxonomic units (vOTUs) were identified, with 99% being novel.

Viruses target key groundwater microbes like Proteobacteria and DPANN archaea.

Viral auxiliary metabolic genes are linked to carbon, nitrogen, and sulfur cycling.

Abstract

Groundwater ecosystems harbor diverse microbial communities adapted to energy-limited, light-deprived conditions, yet the role of viruses in these environments remains poorly understood. Here, we analyzed 1.24 terabases of metagenomic and metatranscriptomic data from seven wells in the Hainich Critical Zone Exploratory (CZE) to characterize groundwater viromes. We identified 257,252 viral operational taxonomic units (vOTUs) (≥ 5 kb), with 99% novel at order, family and genus levels against global ocean, freshwater and/or other publicly available datasets. In silico host predictions suggest that vOTUs primarily targeted Proteobacteria, Candidate Phyla Radiation (CPR) bacteria, and DPANN archaea, which reflects abundant and active groundwater microbial members. Patterns of virus-host abundance ratios, CRISPR-spacers, and prophage screening suggest the potential for multi-layer interactions involving CPR/DPANN lineages, their hosts, and viruses. Additionally, we identified 289 KEGG metabolic modules, 31.1% of which were targeted by 3378 vOTUs encoded auxiliary metabolic genes (AMGs) linked to carbon, nitrogen, and sulfur cycling. These findings provide a baseline for exploring how viruses influence microbial community dynamics, metabolic reprogramming and nutrient cycling in groundwater.

Groundwater viruses are less well studied. Here, using large-scale sequencing, the authors uncover extensive, largely uncharacterized viral diversity in groundwater, showing that viruses infect dominant microbes, encode genes linked to carbon, nitrogen and sulfur pathways, and thus shape subsurface microbial communities.

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