Analysis of the anaerobic digestion metagenome under environmental stresses stimulating prophage induction

Abstract

Background The viral community has the potential to influence the structure of the microbiome and thus the yield of the anaerobic digestion process. However, the virome composition in anaerobic digestion is still under-investigated. A viral induction experiment was conducted on separate batches undergoing a series of DNA-damaging stresses, in order to coerce temperate viruses to enter the lytic cycle. Results The sequencing of the metagenome revealed a viral community almost entirely composed of tailed bacteriophages of the order Caudovirales. Following a binning procedure 1,092 viral and 120 prokaryotic genomes were reconstructed, 64 of which included an integrated prophage in their sequence. Clustering of coverage profiles revealed the presence of species, both viral and microbial, sharing similar reactions to shocks. A group of viral genomes, which increase under organic overload and decrease under basic pH, uniquely encode the yopX gene, which is involved in the induction of temperate prophages. Moreover, the in-silico functional analysis revealed an enrichment of sialidases in viral genomes. These genes are associated with tail proteins and, as such, are hypothesised to be involved in the interaction with the host. Archaea registered the most pronounced changes in relation to shocks and featured behaviours not shared with other species. Subsequently, data from 123 different samples of the global anaerobic digestion database was used to determine coverage profiles of host and viral genomes on a broader scale. Conclusions Viruses are key components in anaerobic digestion environments, shaping the microbial guilds which drive the methanogenesis process. In turn, environmental conditions are pivotal in shaping the viral community and the rate of induction of temperate viruses. This study provides an initial insight into the complexity of the anaerobic digestion virome and its relation with the microbial community and the diverse environmental parameters.

Presence and role of viruses in anaerobic digestion of food waste under environmental variability

“…Viruses are being taken into account in the regulation of community composition and elemental cycling in ecosystems [43]. At present, few studies have been conducted to characterize the presence of viruses in AD systems [1,2,49,50]. The presence of abundant microbial populations in ADFW enables complex material metabolism, but the role of viruses in ADFW is still poorly understood.…”

Decoding Microbial Responses to Ammonia Shock Loads in Biogas Reactors through Metagenomics and Metatranscriptomics

“…The pH was determined after sampling with a pH meter (HI2020–02, HANNA instruments, USA). VFA measurements were performed in a gas chromatograph (GC-2010, Shimadzu, Japan) equipped with a Flame Ionization Detector (FID) . The compounds were separated by a capillary column (ZB-FFAP, 30m, 0.53 mm I.D.…”

“…Furthermore, essential process indicators of biogas production and composition, as well as intermediate metabolites (VFA) were monitored throughout the entire experimental period. The measurement of the daily biogas production was carried out using a water replacement gas meter, and methane content was determined using a gas chromatograph (GC-2014, Shimadzu, Japan) equipped with a thermal conductivity detector (TCD) based on the protocol described by Rossi et al (2022) . The pH was determined after sampling with a pH meter (HI2020–02, HANNA instruments, USA).…”

“…The measurement of the daily biogas production was carried out using a water replacement gas meter, and methane content was determined using a gas chromatograph (GC-2014, Shimadzu, Japan) equipped with a thermal conductivity detector (TCD) based on the protocol described by Rossi et al (2022). 15 The pH was determined after sampling with a pH meter (HI2020−02, HANNA instruments, USA). VFA measurements were performed in a gas chromatograph (GC-2010, Shimadzu, Japan) equipped with a Flame Ionization Detector (FID).…”

A global virome of methanogenic archaea highlights novel diversity and adaptations to the gut environment

“…Methylarchaeales 18,19 ), in the Methanotecta (Methanonatronarchaeia 20 , Archaeoglobales 21 , Methanoliparales 16 , Metheno orentales 22 ), in the Diaforarchaea (Methanomassiliicoccales 23 ) and in the Acherontia (Nuwarchaeales_NM3 16 , Methanofastidiosa 24 ). Methanogenic archaea thrive in diverse arti cial and natural anoxic environments covering an extensive range of salinity and temperatures: freshwater and saline sediments 20,25,26 , peatlands 27 , terrestrial aquifers 28 , hydrothermal vents 29,30 , biogas reactors 31,32 , digesters [33][34][35][36][37] , wastewater treatment plants [38][39][40][41][42] , oil facilities 43 and coal seam 44 . Methanogens contribute to climate change through the production of a powerful greenhouse gas, participate in the complete degradation of organic matter in many anoxic environments through their interaction with fermentative bacteria, and are used in industry to transform biowaste into biogas.…”