Diversity and potential biogeochemical impacts of viruses in bulk and rhizosphere soils

Abstract

Summary Viruses can affect microbial dynamics, metabolism and biogeochemical cycles in aquatic ecosystems. However, viral diversity and functions in agricultural soils are poorly known, especially in the rhizosphere. We used virome analysis of eight rhizosphere and bulk soils to study viral diversity and potential biogeochemical impacts in an agro‐ecosystem. The order Caudovirales was the predominant viral type in agricultural soils, with Siphoviridae being the most abundant family. Phylogenetic analysis of the terminase large subunit of Caudovirales identified high viral diversity and three novel groups. Viral community composition differed significantly between bulk and rhizosphere soils. Soil pH was the main environmental driver of the viral community structure. Remarkably, abundant auxiliary carbohydrate‐active enzyme (CAZyme) genes were detected in viromes, including glycoside hydrolases, carbohydrate esterases and carbohydrate‐binding modules. These results demonstrate that virus‐encoded putative auxiliary metabolic genes or metabolic genes that may change bacterial metabolism and indirectly contribute to biogeochemical cycling, especially carbon cycling, in agricultural soil.

Viral Abundance and Diversity of Production Fluids in Oil Reservoirs

“…In this study, the contigs identified as virus ranged from 21.93 to 75.37%, but the majority (24.63 to 78.07%) of contigs still could not be identified by comparison to the known virosphere (based on the NT database). This phenomenon has been reported previously for viromes in other environments, including soil [ 5 , 10 ], marine [ 17 ], freshwater [ 54 ], etc. These contigs that originate from viruses but do not align to any reference virus sequence have been referred to as “viral dark matter” [ 55 ].…”

“…These contigs that originate from viruses but do not align to any reference virus sequence have been referred to as “viral dark matter” [ 55 ]. Only 19.24–29.91% of contigs showed the similarity to known phages, which was far lower than marine [ 17 ], tropical freshwater [ 54 ] and soil [ 5 , 10 ]. In contigs identified as viruses, dominant viral families with relative abundance more than 1% included Myoviridae , Siphoviridae , Podoviridae , Herpesvirales , Ackermannviridae , Mimivirdae and Phycodnaviridae , which mainly belonged to tailed phages ( Myoviridae , Siphoviridae , and Podoviridae ,).…”

“…In addition, many viruses are able to integrate their genome into their host chromosome and act as biological agents for horizontal gene transfer through lysogenic cycles contributing to microbial evolution. Although a lot of research has been conducted regarding viral ecology in soil [ 9 , 10 , 11 , 12 , 13 , 14 , 15 ], marine [ 4 , 8 , 16 , 17 , 18 ], river [ 19 ], wet-land [ 20 ] and paddy [ 21 ] environments, little effort has been made to study viral populations and viral communities in the oil reservoir. Microbial ecology in oil reservoirs mainly focuses on the relationship between injected and indigenous microbes, and the effects of injected nutrients and environmental factors on microbes and microbial community composition in the reservoir.…”

Distribution of soil viruses across China and their potential role in phosphorous metabolism

“…In the genomes of globally abundant ocean viruses, more than two hundred viral-encoded AMGs have been identi ed [8], including carbon, nitrogen, sulfur, and P cycle related genes. However, as far as we know, only four types of viral AMGs (trzN [25], phoH [11], RNR [11] and CAZyme [9,26]) have been identi ed in terrestrial ecosystems. Among them, only the phoH gene is presumed to belong to the Pho regulon and to regulate P uptake and metabolism under low-phosphate conditions [27].…”

Tracking Double-Stranded DNA Bacteriophages and Their Hosts in a Deep Freshwater Lake by Integrating Metagenomics and The Hi-C Technique

“…However, the rapid development of viral metagenomics and bioinformatics has provided an opportunity to overcome these obstacles [5,6]. In recent years, large amounts of viral genomes, most of which are novel bacteriophages, have been identi ed from a variety of environments, such as marine environments [7,8], freshwater environments [9], hot spring mats [10], rhizosphere soils [11], and mangroves [12]. The ndings of these studies indicated that bacteriophages interacting with their hosts (bacteria and archaea), acted as key partners in multiple ecosystems.…”