Low-level predation by lytic phage phiIPLA-RODI promotes biofilm formation and triggers the stringent response in Staphylococcus aureus

Abstract

An important lesson from the war on pathogenic bacteria has been the need to understand the physiological responses and evolution of natural microbial communities. Bacterial populations in the environment are generally forming biofilms subject to some level of phage predation. These multicellular communities are notoriously resistant to antimicrobials and, consequently, very difficult to eradicate. This has sparked the search for new therapeutic alternatives, including phage therapy. This study demonstrates that S. aureus biofilms formed in the presence of a non-lethal dose of phage phiIPLA-RODI exhibit a unique physiological state that could potentially benefit both the host and the predator. Thus, biofilms formed under phage pressure are thicker and have a greater DNA content. Also, the virus-infected biofilm displayed major transcriptional differences compared to an untreated control. Significantly, RNA-seq data revealed activation of the stringent response, which could slow down the advance of the bacteriophage within the biofilm. The end result would be an equilibrium that would help bacterial cells to withstand environmental challenges, while maintaining a reservoir of sensitive bacterial cells available to the phage upon reactivation of the dormant carrier population.

Downregulation of Autolysin-Encoding Genes by Phage-Derived Lytic Proteins Inhibits Biofilm Formation in Staphylococcus aureus

“…Biofilms were grown for 24 h at 25°C, supernatant was then removed and replaced with NaPi buffer alone or containing 10.94 g/ml of protein LysH5. Biofilms were then incubated for 30 min before the adhered cells were scraped as previously described (33). Following treatment with RNAprotect (Qiagen), the samples were stored at Ϫ80°C prior to RNA purification.…”

“…Following treatment with RNAprotect (Qiagen), the samples were stored at Ϫ80°C prior to RNA purification. Total RNA from S. aureus samples was isolated as previously described (33). Briefly, cell lysis was performed by mechanical disruption with a FastPrep-24 in a solution of 1:1 phenol-chloroform, glass beads (Sigma), and 80 mM dithiothreitol.…”

Phage or foe: an insight into the impact of viral predation on microbial communities

“…However, such a scenario does not reflect the most common situation in nature, in which bacterial cells may be undergoing different infection stages while others remain uninfected. To our knowledge, only one study so far has examined how phage predation affects the bacterial population transcriptome during a non-synchronized infection [25]; therefore, further research remains necessary in this area. Moreover, techniques like single-cell transcriptomics could reveal differences between the transcriptomes of individual cells in a phage-infected population.…”

“…Unsurprisingly, most studies of bacteria-phage interactions indicate dramatic changes in the host cell metabolism. Regarding energy metabolism, the most widespread response is a downregulation of genes related to the energy status of cells [25][26][27][28][29][30]. Additionally, infection with lytic phages leads to an upregulation of anaerobic respiration genes in L. lactis and E. coli [20,31].…”

A widespread toxin-antitoxin system exploiting growth control via alarmone signalling

“…In this system, PhRel encoded in a prophage protects Mycobacteria from an infection by a second phage. Phage infection has previously been linked to alarmone accumulation and stringent response in bacteria (48)(49)(50). Presumably this is an example of a so called abortive infection mechanism(51), where infected hosts are metabolically restricted, but the larger population is protected.…”