Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios

Abstract

Background: Bacteriophages, the viruses infecting bacteria, are biological entities that can control their host populations. The ecological relevance of phages for microbial systems has been widely explored in aquatic environments, but the current understanding of the role of phages in terrestrial ecosystems remains limited. Here, our objective was to quantify the extent to which phages drive the assembly and functioning of soil bacterial communities. We performed a reciprocal transplant experiment using natural and sterilized soil incubated with different combinations of two soil microbial communities, challenged against native and non-native phage suspensions as well as against a cocktail of phage isolates. We tested three different community assembly scenarios by adding phages: (a) during soil colonization, (b) after colonization, and (c) in natural soil communities. One month after inoculation with phage suspensions, bacterial communities were assessed by 16S rRNA amplicon gene sequencing. Results: By comparing the treatments inoculated with active versus autoclaved phages, our results show that changes in phage pressure have the potential to impact soil bacterial community composition and diversity. We also found a positive effect of active phages on the soil ammonium concentration in a few treatments, which indicates that increased phage pressure may also be important for soil functions. Conclusions: Overall, the present work contributes to expand the current knowledge about soil phages and provide some empirical evidence supporting their relevance for soil bacterial community assembly and functioning.

Influence of Non-canonical DNA Bases on the Genomic Diversity of Tevenvirinae

“…The influence of ecological niches on the evolutionary divergence of viruses was demonstrated earlier for T4-related phages (distinguished in the literature as a superfamily), Far-T4-related phages and other bacterial viruses – on the basis of data obtained from metagenomes, metaviromes and phage genomes from various sources ( Desplats and Krisch, 2003 ; Filée et al, 2005 ; Bellas and Anesio, 2013 ; Roux et al, 2015 ; Braga et al, 2020 ). However, for some phages, the isolation-related features of their ecological niches are not the only factors that can drive evolutionary divergence in the phage groups.…”

Novel virocell metabolic potential revealed in agricultural soils by virus‐enriched soil metagenome analysis

“…Accordingly, it has been proposed that terrestrial viruses also play major roles in their respective ecosystems (Kuzyakov and Mason‐Jones, 2018; Pratama et al ., 2020). Recent research revealed that soil viruses can infect key carbon cyclers (Emerson et al ., 2018; Trubl et al ., 2018), encode AMGs associated with biomass degradation (Emerson et al ., 2018; Trubl et al ., 2018; Jin et al ., 2019) and impact nitrogen availability in soil (Braga et al ., 2020). However, the low prevalence of viral sequences in metagenomes and the lack of universal marker genes have hampered the understanding of the diversity and the roles of viruses in the environment particularly in soil ecosystems compared with marine ecosystems.…”

“…To expand our knowledge on soil viruses and their putative contributions to soil microbial processes, we performed a shotgun metagenomic analysis of virus‐enriched soil microbiomes using tangential flow filtration (TFF) system of two French agricultural soil suspensions. Using a dataset that was obtained in a previous study (Braga et al ., 2020) we refined the quality of the viral genomes and conducted a customized taxonomic and host prediction analysis, followed by functional annotation of genes and mining of AMGs (see Supplementary Information). Briefly, soil samples from two INRA experimental farms (Dijon and Montpellier) were sieved (4 mm), homogenized and stored at −20 °C prior to downstream procedures.…”

Ecology of active viruses and their bacterial hosts in frozen Arctic peat soil revealed with H218O stable isotope probing metagenomics

“…Soils hold an enormous viral reservoir, but we know remarkably little about their diversity, activity, host interactions, lysis-induced C-cycling, and persistence as compared to other environments [18, 19]. Viruses can affect soil C cycling by stopping microbial metabolism during lytic infections and releasing cell-derived nutrients into the environment [20]. These nutrients can either fuel other organisms’ metabolism or be stabilized via entombing effects [21].…”