Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities

Abstract

Viruses are abundant yet understudied members of soil environments that influence terrestrial biogeochemical cycles. Here, we characterized the dsDNA viral diversity in biochar-amended agricultural soils at the pre-planting and harvesting stages of a tomato growing season via paired total metagenomes and viromes. Size fractionation prior to DNA extraction reduced sources of non-viral DNA in viromes, enabling the recovery of a vaster richness of viral populations (vOTUs), greater viral taxonomic diversity, broader range of predicted hosts, and better access to the rare virosphere, relative to total metagenomes, which tended to recover only the most persistent and abundant vOTUs. Of 2,961 detected vOTUs, 2,684 were recovered exclusively from viromes, while only three were recovered from total metagenomes alone. Both viral and microbial communities differed significantly over time, suggesting a coupled response to rhizosphere recruitment processes and nitrogen amendments. Viral communities alone were also structured along a spatial gradient. Overall, our results highlight the utility of soil viromics and reveal similarities between viral and microbial community dynamics throughout the tomato growing season yet suggest a partial decoupling of the processes driving their spatial distributions, potentially due to differences in dispersal, decay rates, and/or sensitivities to soil heterogeneity.

Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations

“…Considering all assembled contigs ≥ 10 kbp, only 0.8% of the metagenomic contigs were classified as viral after passing them through viral prediction software (see methods), relative to 16% of the virome contigs. This ~20fold improvement is consistent with our observed ~30-fold improvement in viral contig recovery from viromes relative to total metagenomes in agricultural soils [35], and similar differences in the composition of metagenomes and viromes have been reported from grassland soils [52].…”

“…We speculate that this low level of taxonomic affiliation may be related to the inclusion of more vOTUs from viromes in the current study, relative to the previous work that was focused almost exclusively on viral recovery from total metagenomes. Viromes tend to access more of the rare virosphere [35] recovered from a single study and/or location so far. In total, 9.3% of the soil VCs, containing 8.2% of the vOTUs, were exclusively found in SPRUCE peatlands.…”

“…To investigate similarities between genus-level VCs from soil and aquatic (marine and freshwater) ecosystems, 232,116 vOTUs from our PIGEON database (32,346 soil vOTUs [10,15,31,35], 190,502 vOTUS from marine environments [31,88,89], and 11,869 vOTUs from freshwater environments [31]) were clustered into 78,213 VCs (Table S11). Of the soil VCs, 1.9% shared a cluster with one or both aquatic systems, indicating a small amount of genus-level similarity between aquatic and soil viruses (Fig.…”

“…In addition to mining omic data for viral signatures, laboratory enrichment of viral particles prior to sequencing can allow for the generation and analysis of viral size-fraction metagenomes (viromes) from soil. This approach has recently been paired with high-throughput sequencing, revealing more comprehensive insights into soil viral ecology [13,15,34,35], including in thawing permafrost peatlands.…”

“…Although we now have an array of laboratory and bioinformatics methods for soil viral ecology [7,15,23,31,34,[46][47][48][49][50][51], we lack a thorough comparative understanding of these approaches and best practices. As one specific example, viral size-fraction metagenomes (viromes) from grassland and agricultural soils have been shown to be substantially enriched in viral and ultrasmall cellular organismal DNA, compared to total metagenomes that tend to be more enriched in DNA from cellular organisms too large to easily pass through the 0.2 µm filters used for viral enrichment [35,52]. Although these results would suggest that viromes may be more appropriate than total metagenomes for studying viral communities, the generalizability of this trend across soils and in other ecosystems is unknown.…”