Viral and Bacterial Communities Collaborate through Complementary Assembly Processes in Soil to Survive Organochlorine Contamination

Abstract

The interaction between viral communities and microbial hosts has been studied extensively, and the viral community affects host community metabolic function through AMGs. Microbial community assembly is the process by which species colonize and interact to establish and maintain communities.

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

“…AMGs of interest that passed manual curation included genes predicted to be involved in carbohydrate metabolism, methane metabolism, and sulfur metabolism (Table 6). The CA_2019 dataset included an AMG predicted to have a role in degradation of organochlorine compounds, which has been observed in previous studies [23,24]. Numerous putative AMGs were also predicted in the putative megaphages - full details of VIBRANT-predicted AMGs encoded by these putative megaphages are available in Table S4.…”

“…We used vConTACT2 [44] to determine the extent of relatedness between viral genomes in our study. vConTACT2 uses shared protein clusters (PCs) to delineate viral clusters (VCs) and was run against all ≥10 kbp viral elements (34,499) detected in our samples, along with a total of 45,523 viral elements from IMG/VR [45] detected in either wastewater samples (24,982) or groundwater samples (20,541), and the "Prokaryotic Viral Refseq version 85 with ICTV-only taxonomy" reference database (2,617 reference sequences) (Figure S1). While some similarity was observed between landfill viral elements and those from wastewater and groundwater, landfill viral elements frequently formed their own clusters with limited overlap with viral elements from other sites.…”

“…During infections, viruses may augment or modify the metabolism of their hosts through AMGs [17][18][19][20][21], including contaminant modification and degradation. Recent research has identified viruses encoding arsenic resistance and transporter genes in arsenic-contaminated paddy soils [22], and showed viruses aiding their hosts' survival in organochlorine contaminated soils with AMGs involved in organochlorine degradation [23,24]. This phenomenon of contaminant modification/degradation genes being provisioned by viruses to their hosts has yet to be examined in municipal waste sites, which are highly and heterogeneously contaminated systems.…”

Viromes of Coastal Waters of the North Caspian Sea: Initial Assessment of Diversity and Functional Potential

“…Bacteriophages are significantly more abundant in aquatic ecosystems than other life forms [7], with an approximate concentration of approximately 10 billion particles per liter in surface waters [8,9], although their abundance varies depending on ocean depth, temperature [10], latitude [11] and phytoplankton bloom development [12]. Marine viruses play an important role in regulating bacterial abundance, forming the structure of the microbial community and modifying the genetic diversity of microorganisms through horizontal transfer of genes [13]. Viral lysis mediates the transfer of organic matter between living biomass and the pool of dissolved organic carbon through a viral shunt [14,15].…”