Phages in vermicomposts enrich functional gene content and facilitate pesticide degradation in soil

Unraveling phase-dependent variations of viral community, virus-host linkage, and functional potential during manure composting process

The temporal dynamics of bacterial and fungal communities significantly impact the manure composting process, yet viral communities are often underexplored. Bulk metagenomes, viromes, metatranscriptomes, and metabolomes were integrated to investigate dynamics of double-stranded DNA (dsDNA) virus and virus-host interactions throughout a 63-day composting process. A total of 473 viral operational taxonomic units (vOTUs), predominantly Caudoviricetes, showed distinct phase-dependent differentiation. In phase I (initial-mesophilic), viruses targeted Gammaproteobacteria and Firmicutes, utilizing restriction-modification (RM) systems. In phase II (thermophilic-maturing), viruses infected Alphaproteobacteria, Chloroflexi, and Planctomycetes, employing CRISPR-Cas systems. Lysogenic and lytic viruses exerting differential effects on bacterial pathogens across phases. Additionally, six types of auxiliary metabolic genes (AMGs) related to galactose and cysteine metabolisms were identified. The homologous lineages of AMGs with bacterial genes, along with the significant temporal correlation observed between virus-host-metabolite interactions, underscore the critical yet often overlooked role of viral communities in modulating microbial metabolisms and pathogenesis within composting ecosystems.

Bio-transformation of poultry litter and activated sewage sludge to produce biomixtures for the remediation of water polluted with pesticides

The aim of this study was to formulate novel biomixtures with the ability to dissipate globally used pesticides. For this, an effective stabilization of two wastes, poultry litter and activated sewage sludge, was achieved through a combination of composting and vermicomposting, with the aid of the earthworm Eisenia fetida. Hence, two different mixtures were prepared combining the wastes with and without the addition of sewage sludge, and their physicochemical and microbiological characterization was examined during both processes. Earthworms reproduction was promoted by more than fourteen times the initial number of individuals introduced. This step made it possible to obtain substrates rich in organic matter, stable and non-pathogenic. The resulting vermicomposted substrates (V-C1 and V-C2) were used to produce two different biomixtures with wheat stubble (WS) and soil (S): SWSV-C1 and SWSV-C2, and they were tested for the remediation of a solution of five pesticides (2,4-D, cypermethrin, imidacloprid, acetochlor and dimethoate) in a 119-days assay. Comparisons were made with a WS-only biomixture (SWS) and a soil control. All biomixtures were more successful in dissipating the pesticides than soil; 2,4-D, dimethoate, and acetochlor degradation reached more than 99% in the three biomixtures after 28-56 days of assay. Biomixtures containing either vermicomposts acted faster than SWS, particularly for 2,4-D, dimethoate and cypermethrin. The total microbial activity was found to be higher in the two biomixtures containing vermicompost, which can be linked to their enhanced performance in the degradation of pesticides. Although the germination of Lactuca sativa proved that neither of the three spent biomixtures were phytotoxic at the end (germination index >60%), only SWSV-C1 and SWSV-C2 proved to be safe for the survival of E. fetida. This work confirms that vermicompost improves the success of biomixtures, not only in terms of pesticide removal, but also providing non-toxic spent biomixtures.

The role of rhizosphere phages in soil health

While the One Health framework has emphasized the importance of soil microbiomes for plant and human health, one of the most diverse and abundant groups-bacterial viruses, i.e. phages-has been mostly neglected. This perspective reviews the significance of phages for plant health in rhizosphere and explores their ecological and evolutionary impacts on soil ecosystems. We first summarize our current understanding of the diversity and ecological roles of phages in soil microbiomes in terms of nutrient cycling, top-down density regulation, and pathogen suppression. We then consider how phages drive bacterial evolution in soils by promoting horizontal gene transfer, encoding auxiliary metabolic genes that increase host bacterial fitness, and selecting for phage-resistant mutants with altered ecology due to trade-offs with pathogen competitiveness and virulence. Finally, we consider challenges and avenues for phage research in soil ecosystems and how to elucidate the significance of phages for microbial ecology and evolution and soil ecosystem functioning in the future. We conclude that similar to bacteria, phages likely play important roles in connecting different One Health compartments, affecting microbiome diversity and functions in soils. From the applied perspective, phages could offer novel approaches to modulate and optimize microbial and microbe-plant interactions to enhance soil health.

The insights into the phage communities of fermented foods in the age of viral metagenomics

Phages play a critical role in the assembly and regulation of fermented food microbiome through lysis and lysogenic lifestyle, which in turn affects the yield and quality of fermented foods. Therefore, it is important to investigate and characterize the diversity and function of phages under complex microbial communities and nutrient substrate conditions to provide novel insights into the regulation of traditional spontaneous fermentation. Viral metagenomics has gradually garnered increasing attention in fermented food research to elucidate phage functions and characterize the interactions between phages and the microbial community. Advances in this technology have uncovered a wide range of phages associated with the production of traditional fermented foods and beverages. This paper reviews the common methods of viral metagenomics applied in fermented food research, and summarizes the ecological functions of phages in traditional fermented foods. In the future, combining viral metagenomics with culturable methods and metagenomics will broaden the scope of research on fermented food systems, revealing the complex role of phages and intricate phage-bacterium interactions.