Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil

Abstract

Viruses impact nearly all organisms on Earth, with ripples of influence in agriculture, health and biogeochemical processes. However, very little is known about RNA viruses in an environmental context, and even less is known about their diversity and ecology in the most complex microbial system, soil. Here, we assembled 48 individual metatranscriptomes from four habitats within a soil sampled over a 22-day time series: rhizosphere alone, detritosphere alone, a combination of the two, and unamended soil (four time points and three biological replicates per time point). We resolved the RNA viral community, uncovering a high diversity of viral sequences. We also investigated possible host organisms by analyzing metatranscriptome marker gene content. Based on viral phylogeny, much of the diversity was Narnaviridae that parasitize fungi or Leviviridae that infect Proteobacteria. Both host and viral communities appear to be highly dynamic, and rapidly diverged depending on experimental conditions. The viral communities were structured based on the presence of litter, while putative hosts appeared to be impacted by both the presence of litter and roots. A clear time signature from Leviviridae and their hosts indicated that viruses were replicating. With this time-resolved analysis, we show that RNA viruses are diverse, abundant and active in soil. Their replication causes host cell death, mobilizing carbon in a process that represents a largely overlooked component of carbon cycling in soil.

Characterization of the Gut DNA and RNA Viromes in A Cohort of Chinese Residents and Visiting Pakistanis

“…To identify RNA viruses, the assembled contigs (> 500 bp) was aligned to the reference RNA virus proteins downloaded from GenBank database using DIAMOND (blastx e-value < 1e-5). We also identi ed the RNA viral contigs by searching the RNA-dependent RNA polymerase genes (RdRp genes, referred from Evan et al [80]) using a Hidden Markov Model approach [81]. Then, the RNA viral sequences were clustered based on 95% identity and 90% coverage of the sequence.…”

Stable isotope informed genome-resolved metagenomics uncovers potential trophic interactions in rhizosphere soil

“…A. fatua plants were grown in a continuously regenerated 13 CO2 environment. One plant was harvested after six weeks and a second after nine weeks.…”

“…DNA was extracted from both the rhizosphere and bulk soil samples. We compared the density separation of the rhizosphere DNA to the bulk soil DNA to identify un-enriched DNA (light), a mixture of enriched and unenriched DNA (middle), and highly 13 C-enriched (heavy) then these fractions were shotgun sequenced (Supplemental figure 1 and Supplemental table 1). After assembly of the individual metagenomes, it appeared that the heavier fractions (middle and heavy) had larger assemblies and higher N50 values than the assemblies of the more complex light fractions (Supplemental table 1).…”

“…Such biosynthetic pathways hold technological relevance but are also fundamental for soil ecology, as their products could mediate inter-organismal interactions, including offensive interactions via antibiotics, interorganism and mineral-interactions via siderophores, and signaling compounds (10,11). While there has been a surge of interest in viral diversity and ecology, there have been relatively few studies documenting bacterial-phage interactions in soil (12)(13)(14). Also present in soil are fungi, protists and larger organisms that have been documented via 18S rRNA gene sequencing (15,16) and more classical methods (17,18).…”

“…To better understand the soil inter-organismal interactions that are initiated by the input of plant-derived rhizodeposits, we combined stable isotope probing and genome resolved metagenomics. We grew common wild oat grass, Avena fatua, for six and nine weeks in a 13 CO2 enriched atmosphere and tracked the isotopically enriched plant carbon as it was released to the surrounding soil community via exudation, decay of root biomass, and direct biotic transfer through pathogen attack. Over the course of our experiment, we expected the plant-derived carbon to move through trophic levels, including primary consumers, predators, parasites, saprotrophs, and their phage.…”