Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France.
Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France.
ISME J. 2023 Oct;17(10):1552-1563. doi: 10.1038/s41396-023-01431-y. Epub 2023 May 11.
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.
一般认为，地球上的病毒数量至少是细胞数量的十倍。病毒与微生物的比例（VMR）主要基于荧光标记的病毒样颗粒的计数。然而，这些计数排除了细胞内病毒，并且可能包括假阳性（含有 DNA 的囊泡、基因转移剂、非特异性染色的惰性颗粒）。在这里，我们开发了一种基于宏基因组的 VMR 估计（mVRM），通过使用主要衣壳蛋白（MCP）基因和细胞通用单拷贝基因（USCGs）的归一化 RPKM（每百万映射宏基因组读数的基因序列每千碱基的读数）计数来计算所有复制周期（病毒体、细胞内裂解和溶源）阶段的 DNA 病毒，分别作为病毒和细胞计数的替代物。在使用具有递增 VMR 的模拟宏基因组对该策略进行基准测试后，我们推断了不同生物群落中的 mVMR。为了正确估计水生生态系统中的 mVMR，我们从淡水、海水和太阳盐沼池塘中的共存细胞和病毒部分（>50 kDa-200 µm 大小范围）生成了宏基因组（10 个宏基因组，2 个对照 metaviromes）。在淡水中，病毒数量比细胞多约 13 倍，在海洋和咸水中的浮游生物中多约 2-4 倍。然而，在包括微生物垫、微生物岩、土壤、淡水和海洋沉积物以及后生动物相关微生物组在内的另外 121 个多样化的非水生宏基因组中，病毒的数量平均比细胞多不到两倍。尽管病毒可能是地球上最多样化的生物实体，但它们的全球数量可能比以前估计的更接近细胞数量。
