CRISPR-resolved virus-host interactions in a municipal landfill include non-specific viruses, hyper-targeted viral populations, and interviral conflicts

Abstract

Viruses are the most abundant microbial guild on the planet, impacting microbial community structure and ecosystem services. Viruses are specifically understudied in engineered environments, including examinations of their host interactions. We examined host-virus interactions via host CRISPR spacer to viral protospacer mapping in a municipal landfill across two years. Viruses comprised ~ 4% of both the unassembled reads and assembled basepairs. A total of 458 unique virus-host connections captured hyper-targeted viral populations and host CRISPR array adaptation over time. Four viruses were predicted to infect across multiple phyla, suggesting that some viruses are far less host-specific than is currently understood. We detected 161 viral elements that encode CRISPR arrays, including one with 187 spacers, the longest virally-encoded CRISPR array described to date. Virally-encoded CRISPR arrays targeted other viral elements in interviral conflicts. CRISPR-encoding proviruses integrated into host chromosomes were latent examples of CRISPR-immunity-based superinfection exclusion. The bulk of the observed virus-host interactions fit the one-virus-one-host paradigm, but with limited geographic specificity. Our networks highlight rare and previously undescribed complex interactions influencing the ecology of this dynamic engineered system. Our observations indicate landfills, as heterogeneous contaminated sites with unique selective pressures, are key locations for atypical virus-host dynamics.

Discarded diversity: Novel megaphages, auxiliary metabolic genes, and virally encoded CRISPR-Cas systems in landfills

“…This study makes use of 27 metagenomes that were sequenced from samples from three distinct landfills. Fourteen metagenomes were sequenced from an active municipal landfill and adjacent aquifer in Southern Ontario (SO), sampled twice one year apart (July 2016 [SO 2016] and October 2017 [SO 2017]) and described previously [9,35]. Nine metagenomes were from a northeastern United States active municipal landfill (NEUS) in which nine distinct cells, units in which waste is held within the landfill, were sampled in February 2019 as described previously [36].…”

“…Bacteriophages are predicted to be quite host specific, but recent studies have suggested the presence of phages with diverse host ranges in different environments. In research on both isolated phages [8] and those identified in silico, bacteriophages have been shown or predicted to infect across distinct bacterial phyla [1,[9][10][11] and domains of life [2,8,11]. While the mechanisms of viral infection across organisms from different phyla or domains are likely very complex and difficult to resolve without wet-lab experiments, the potential presence of such viruses with large host ranges and their isolation can be important for biotechnological applications including phage therapy.…”

“…There are multiple computational methods to predict microbial hosts of viruses [12,13], with CRISPR spacer to viral protospacer matching having relatively low sensitivity, but high specificity [12]. In municipal waste systems, viruses that infect bacteria and archaea are predicted to have diverse infection dynamics with their hosts based on CRISPR spacer to virus protospacer matching [9]. The open questions remain of whether the notable virus-host interactions observed in a single municipal waste site, such as hyper-targeted viral elements, interviral conflicts, and putative cross-phylum-infecting phages [9] are consistent across other municipal waste sites, and whether these interactions are underlain by conserved CRISPR array architectures across geographically distant sites.…”

“…Discovery of new, divergent Cas proteins and CRISPR-Cas system assemblages is of interest to address these limitations, in hopes of broadening the current application space [25] . Virus-encoded CRISPR arrays and CRISPR-Cas systems have been identified from a variety of environments [9,16,[26][27][28][29][30][31][32][33] and are involved in crippling host viral defense systems [28]; regulating host transcription and translation [16]; CRISPR-Cas system inhibition [31]; and interviral conflicts [9,[31][32] . Recent discoveries of some of the most streamlined CRISPR-Cas systems from viruses [16,33,34] established viruses as a potential hot spot for new CRISPR-Cas systems with biotechnological value.…”

Inferring strain-level mutational drivers of phage-bacteria interaction phenotypes

“…However, predicting strain-specific interactions remains a difficult task, particularly because taxonomic markers are known to be a poor proxy for infection profiles [ (Sullivan NJ, 2003), (Kauffman KM, 2022)]. Recent studies have shown some improvement in resolving strain-specific interaction phenotypes, e.g., by using CRISPR spacers and metagenomic data to identify recent phage infection [ (Simon Roux, 2021), (Szabo RE., 2022), (George, 2023)] or by co-clustering phage and bacteria mutations, respectively, amongst strains that tend to interact as a means to identify associated gene or sequence differences [ (Kauffman KM, 2022)].…”