Soil phage–host associations are revealed by Hi-C metagenome sequencing
Soils are rich in bacteriophages. But most are uncharacterized, and we don’t know who their hosts are. Here, phage-host connections are directly captured using high-throughput chromosomal conformation capture (Hi–C). Phage infections may play a significant role in the interactions between the soil bacterial population and certain hosts, as indicated by their elevated centralities in microbial community co-occurrence networks. After a two week incubation period in soil drying, less viral transcriptional activity and higher average viral replication per host (VPH) was found that suggest a rise in lysogenic infections. The range of known phage hosts is also changed by soil drying. Prior to drying, there was a substantial negative association between VPH and population plenty, indicating that more powerful lytic infections cause more host deaths, which in turn had an inverse effect on host abundance. This work directly captures particular phage-host interactions, offering empirical proof of phage-mediated microbial population fluctuations in soil.
With values of 107 to 1010 viral-like particles per gram of soil, viruses are extremely prevalent in soil and have an impact on the control of host population dynamics. According to recent research, bacteriophages, also known as phages, prefer a temperate (lysogenic) lifestyle in which they live as prophages in their bacterial hosts in dry soils. In contrast, phages have a tendency to become lytic in damp soil conditions, where they vigorously replicate and eliminate their hosts. Changes in lysogenic vs lytic lifestyles can have a big effect on host abundances, which in turn affects the makeup and functionality of soil microbes. However, when analyzing the intricate microbial community in soil, it is still difficult to determine which phage infects that hosts or hosts. A more precise understanding of the effects of soil viruses on the soil requires this knowledge.
The majority of the techniques used now to identify phage-host couples rely on circumstantial sequence-based data. These techniques involve pairing CRISPR spacers to phage genomes6,7 and employing alignment-dependent (like VPF-Class8) or alignment-free (like WIsH9, VHM10, and PHP11) approaches to look for homology between phage and host genomes. These methods have helped to shed light on which host taxa soil phages may infect. Even while some researches show that the Hi-C technique can identify phage-host interactions in complicated samples like soil, there is still room for improvement through additional experimental modification. This will make it possible for future research to investigate the Hi-C approach’s applicability in identifying viral infections in various soil systems and environments in nature. It is highlighted that the Hi-C method can also be used to find viruses in the environment that could pose a harm to human health. Hi-C sequencing can be applied to soil, as studies show, and the findings are useful for forecasting how soil viruses may be affected by climate change and the resulting ecological effects.