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. Video Abstract.

Fig. 1

Schematic illustration of the experimental design. The microcosms were destructively sampled 34 days (a and b) or 35 days (c) after phage suspension inoculation. Soil suspensions from soil 1 (S1) and 2 (S2) were filtered to separate the phage fraction (PS1 and PS2) and bacterial fraction (BS1 and BS2). An outgroup with phage isolates named phage cocktail (PC) was also included. The different conditions were compared against a control made with autoclaved phage suspension (red cross) (PS1a, PS2a, and PCa). a During colonization experiment: both phage and bacterial suspensions were inoculated in microcosms made with sterile soil at the same time. b After colonization experiment: the bacterial fraction was inoculated first in the microcosms made with sterile soil, and the phage fraction was inoculated 28 days later. c Natural soils experiment: the phage fraction was inoculated in the microcosms made with the natural soils, 28 days after assembling the pots

Fig. 2

a–c Proportion plots of balance analysis from gneiss showing differentially abundant bacterial groups most affected by phage suspensions on treatments where both alpha and beta diversities where significantly changed (see Table 1). The plots are divided vertically comparing natural vs autoclaved (with red cross) conditions

Fig. 3

Weighted (a) and unweighted (b) UniFrac distance values between each treatment inoculated with active phages and the control inoculated with autoclaved phages. The values represent means with standard deviation and different letters above the bars indicate significant differences (Tukey’s test, p value < 0.05)

Fig. 4

Poisson lognormal model for sparse covariance inference for bacterial abundances. Nodes represent ASVs sized based on degree. Equal superscript red letters indicate that nodes in different networks correspond to the same clade (i.e., same ASV). Edges connecting nodes represent positive (light blue) and negative (red) interactions

Fig. 5

Soil inorganic nitrogen (N) determination. Y-axis indicates NO₃^- and NH₄⁺ by mg N/kg of dried soil. X-axis indicates treatments. BS1: bacterial community from soil 1; BS2: bacterial community from soil 2; S1: natural soil 1; S2: natural soil 2; PS1: phage community from soil 1; PS2: phage community from soil 2; PC: phage cocktail. Y-axis scale of the natural soils (c) is different from the other plots (a and b). *Significant differences in pairwise comparisons (n = 5) between natural phage suspension (blue) vs control autoclaved phage suspension (orange) (Tukey’s HSD test, p ≤ 0.05)