Geochemical constraints on bacteriophage infectivity in terrestrial environments

Abstract

Lytic phages can be potent and selective inhibitors of microbial growth and can have profound impacts on microbiome composition and function. However, there is uncertainty about the biogeochemical conditions under which phage predation modulates microbial ecosystem function, particularly in terrestrial systems. Ionic strength is critical for infection of bacteria by many phages, but quantitative data is limited on the ion thresholds for phage infection that can be compared with environmental ion concentrations. Similarly, while carbon composition varies in the environment, we do not know how this variability influences the impact of phage predation on microbiome function. Here, we measured the half-maximal effective concentrations (EC50) of 80 different inorganic ions for the infection of E. coli with two canonical dsDNA and ssRNA phages, T4 and MS2, respectively. Many alkaline earth metals and alkali metals enabled lytic infection but the ionic strength thresholds varied for different ions between phages. Additionally, using a freshwater nitrate-reducing microbiome, we found that the ability of lytic phages to influence nitrate reduction end-products depended upon the carbon source as well as ionic strength. For all phage:host pairs, the ion EC50s for phage infection exceeded the ion concentrations found in many terrestrial freshwater systems. Thus, our findings support a model where phages most influence terrestrial microbial functional ecology in hot spots and hot moments such as metazoan guts, drought influenced soils, or biofilms where ion concentration is locally or transiently elevated and nutrients are available to support the growth of specific phage hosts.

Systematic and scalable genome-wide essentiality mapping to identify nonessential genes in phages

“…Even though the gene essentiality mapping results are dependent on the experimental settings and conditions used in the assay systems, they do open up interesting questions and avenues to assess the role of nonessential and accessory genes in phage development and infection pathways [ 15 , 17 , 18 ]. By adopting high-throughput CRISPRi assays to map phage gene essentiality in different conditions [ 81 ], it may be possible to study the role of such conditional gene essentiality in phage infection. Furthermore, the simple multiplexability of dCas12a crRNAs (for example, dual crRNAs targeting 2 genes) could enable rapid, systematic investigation of synthetic lethal phage gene pairs.…”

Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates

“…The percentage of wells showing growth was much higher than in the previous isolation round (37% of total wells). Therefore, high-throughput sequencing of the 16S rRNA gene V4/V5 region was performed as previously described [ 39 ] with 600 bp v3 reagents. This step allowed us to select wells containing a single amplicon sequence variant, which were assumed to be clonal cultures.…”

Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B12

“…The 16S rRNA gene V4/V5 region was amplified by PCR and analyzed as previously described in Carlson et al . [ 46 ]. Data for enrichment and microcosm relative abundances are found in Supplementary Tables 3 and 4 .…”