Metagenome-derived virus-microbe ratios across ecosystems

Abstract

It is generally assumed that viruses outnumber cells on Earth by at least tenfold. Virus-to-microbe ratios (VMR) are largely based on counts of fluorescently labelled virus-like particles. However, these exclude intracellular viruses and potentially include false positives (DNA-containing vesicles, gene-transfer agents, unspecifically stained inert particles). Here, we develop a metagenome-based VMR estimate (mVRM) that accounts for DNA viruses across all stages of their replication cycles (virion, intracellular lytic and lysogenic) by using normalised RPKM (reads per kilobase of gene sequence per million of mapped metagenome reads) counts of the major capsid protein (MCP) genes and cellular universal single-copy genes (USCGs) as proxies for virus and cell counts, respectively. After benchmarking this strategy using mock metagenomes with increasing VMR, we inferred mVMR across different biomes. To properly estimate mVMR in aquatic ecosystems, we generated metagenomes from co-occurring cellular and viral fractions (>50 kDa–200 µm size-range) in freshwater, seawater and solar saltern ponds (10 metagenomes, 2 control metaviromes). Viruses outnumbered cells in freshwater by ~13 fold and in plankton from marine and saline waters by ~2–4 fold. However, across an additional set of 121 diverse non-aquatic metagenomes including microbial mats, microbialites, soils, freshwater and marine sediments and metazoan-associated microbiomes, viruses, on average, outnumbered cells by barely two-fold. Although viruses likely are the most diverse biological entities on Earth, their global numbers might be closer to those of cells than previously estimated.

Pleomorphic viruses establish stable relationship with marine hyperthermophilic archaea

“…The virus-to-host ratio fluctuated around 1 ( Fig. 1D ), mirroring the recent metagenome-derived estimates across ecosystems [ 16 ]. To study whether this equilibrium can be destabilized, we challenged A. veneficus cultures with different environmental stressors.…”

Bacterial defenses and their trade-off with growth are not ubiquitous but depend on ecological contexts

“…Bacterial viruses, also known as phages or bacteriophages, represent the most abundant biological entities on Earth. They significantly outnumber bacterial cells across various samples and microbiomes, with ratios reaching up to ∼15-25 fold, as observed in freshwater plankton (López-García et al 2023; Roux and Brum 2023). In environments like seawater, this constant predation results in a substantial daily death rate of bacterioplankton, estimated between 25-40% (Wommack and Colwell 2000; Suttle 2007).…”

Viral communities in millipede guts: Insights into the diversity and potential role in modulating the microbiome

“…To reduce the variation in ribosomal protein genes, the average relative abundances of USCGs at the class level were used as proxies for cell counts. The mVMR was calculated by selecting the top 15 most abundant USCGs, following López‐García et al (2023). For MCPs and RdRp gene identification and taxonomy assignment, geNomad‐annotate (Camargo et al, 2023) was used, employing a marker database for viral classification.…”

“…Metagenomics virus-to-microbe ratios (mVMR) were calculated by searching for the MCP, RdRP and cUSCG genes as proxies for DNA viruses, RNA viruses and cell counts, respectively (L opez-García et al, 2023). Based on that, we considered an mVMR below 1 to be 'low', between 1 and 3 to be 'medium', and above that to be 'high'.…”

“…VMR is traditionally determined by counting virus‐like particles and cells (Parikka et al, 2017), but this method has limitations (Danovaro & Middelboe, 2010; Holmfeldt et al, 2012; Kaletta et al, 2020). Metagenomics VMR (mVMR) offers an alternative and is effective, especially in complex environments like soils and gut ecosystems with prevalent lysogenic phages (López‐García et al, 2023). Predicting the VMR in the millipede gut is important because it holds significance for both millipede health and ecology, serving as an indicator of interactions between viruses and bacteria.…”